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Zhang W, Zhu G, Li N, Wang L, Wang M, Wu Y, Zhao Y, Hu Q, Guo G, Wang X. Label-Free Direct Identification of MicroRNAs Based on a Narrow Constant-Inner-Diameter Emitter Mass Spectrometry Analysis. Anal Chem 2024; 96:8914-8921. [PMID: 38776971 DOI: 10.1021/acs.analchem.3c05437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
MicroRNAs (miRNAs) are a class of endogenous noncoding small RNAs that play important roles in various biological processes and diseases. Direct determination of miRNAs is a cost-efficient and accurate method for analysis. Herein, we established a novel method for the analysis of miRNAs based on a narrow constant-inner-diameter mass spectrometry emitter. We utilized the gravity-assisted sleeving etching method to prepare a constant-inner-diameter mass spectrometry emitter with a capillary inner diameter of 5.5 μm, coupled it with a high-voltage power supply and a high-resolution mass spectrometer, and used it for miRNA direct detection. The method showed high sensitivity and reproducibility for the analysis of four miRNAs, with a limit of detection of 100 nmol/L (170 amol) for the Hsa-miR-1290 analysis. Compared with commercial ion sources, our method achieved higher sensitivity for miRNA detection. In addition, we analyzed the total miRNAs in the A549 cells. The result indicated that both spiked and endogenous miRNAs could be quantified with high accuracy. As a result, this method offers a promising platform for highly sensitive and accurate miRNA analysis. Furthermore, this approach can be extended to the analysis of other small oligonucleotides and holds the potential for studying clinical samples and facilitating disease diagnosis.
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Affiliation(s)
- Wenmei Zhang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Guizhen Zhu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Ning Li
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Liangxia Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Mengying Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Yuanyuan Wu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Yaoyao Zhao
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Qin Hu
- Beijing International Science and Technology, Cooperation Base of Antivirus Drug, Department of Environment and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
- Minzu University of China, Beijing 100081, China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
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Li D, Yao Y, Cheng W, Hou Z, Wang Z, Xiang Y. Self-Priming Cyclic Amplification Accelerating CRISPR Sensor for Sensitive and Specific MicroRNA Analysis with No Background. Anal Chem 2024; 96:1717-1724. [PMID: 38217876 DOI: 10.1021/acs.analchem.3c04866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
In this work, we demonstrate for the first time the application of the phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction for miRNA assays. A self-priming amplification accelerating CRISPR sensor was well-established for sensitive and specific miRNA detection by integrating the PS-THSP reaction and CRISPR/Cas12a system. The sensor consists of three steps: (1) the formation of a complete PS-THSP template in the presence of target miRNA and ligase; (2) the exponential isothermal amplification of the PS-THSP reaction under the action of DNA polymerase; (3) the activation of the CRISPR/Cas12a fluorescence system to generate signals. We used miR-21 as a model target. The sensor can achieve sensitive detection of miR-21 without the involvement of any primers, and the special design of the CRISPR proto-spacer neighbor motif (PAM) sequence effectively avoids the interference of the background signal. In addition, the sensor can not only identify single-base mutant homologous sequences but also show stable performance in complex biological matrices. We have successfully used this sensor to accurately analyze miR-21 in different cell lines and real clinical samples, demonstrating its great potential in clinical diagnosis.
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Affiliation(s)
- Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Yanheng Yao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Wenting Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Zhiqiang Hou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Zhongyun Wang
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, P. R. China
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3
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Norouzi S, Soltani S, Alipour E. Recent advancements in biosensor designs toward the detection of intestine cancer miRNA biomarkers. Int J Biol Macromol 2023:125509. [PMID: 37364808 DOI: 10.1016/j.ijbiomac.2023.125509] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/28/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Cancer diagnosis and treatment have been of broad interest among scientists in the last decades due to the high death rate, widespread occurrence, and recurrence after treatment. The survival rate of cancer patients depends greatly on early detection and appropriate treatments. Therefore developing new technologies applicable to sensitive and specific methods of cancer detection is an inevitable task for cancer researchers. Abnormal miRNA expression is contributed to severe diseases such as cancers and since their expression level and type differ strictly during carcinogenesis and later metastasis and treatments, the improved detection accuracy of these miRNAs would undoubtedly lead to early diagnosis, prognosis, and targeted therapy. Biosensors are accurate and straightforward analytical devices that have had practical applications especially in the last decade. Their domain is still growing through a combination of attractive nanomaterials and amplification methods, leading to innovative biosensing platforms for the efficient detection of miRNAs as diagnostic and prognostic biomarkers. In this review, we will provide the recent developments in biosensors to detect intestine cancer miRNA biomarkers and also discuss the challenges and outcomings of this field.
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Affiliation(s)
| | - Somaieh Soltani
- Pharmacy faculty, Tabriz University of Medical Sciences, Tabriz, Iran.
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Li Z, Zhou J, Wang C, Liu R, Hu J, Lv Y. Isotope-encoded tetrahedral DNA for multiple SARS-CoV-2 variant diagnosis. Chem Sci 2023; 14:6654-6662. [PMID: 37350832 PMCID: PMC10283508 DOI: 10.1039/d3sc01960h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed an unprecedented demand for accurate and cost-effective diagnostic assays to discriminate between different variants. Whilst many bioassays have been successfully demonstrated for SARS-CoV-2 detection, diagnosis of its variants remains challenging and mainly relies on time-consuming and costly sequencing techniques. Herein, we proposed a triplevalent tetrahedral DNA nanostructure (tTDN) with three overhang isotope probes capable of multiplex simultaneous analysis. HV69/70 del (alpha-specific), K417N (beta-specific) and T478K (delta-specific) and omicron with common mutations above of the SARS-CoV-2 S gene were detected selectively with the aid of the TDN scaffold and MNAzyme system, and a sensitive strategy enabling the screening of four kinds of variants of concern (VOC) was achieved.
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Affiliation(s)
- Ziyan Li
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Jing Zhou
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Chaoqun Wang
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
| | - Rui Liu
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University Chengdu 610064 Sichuan China
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Faculty of Medicine & Dentistry, University of Alberta Edmonton T6G 2G3 Alberta Canada
| | - Yi Lv
- Analytical & Testing Center, Sichuan University Chengdu 610064 China
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University Chengdu 610064 Sichuan China
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Zhao M, Wang R, Yang K, Jiang Y, Peng Y, Li Y, Zhang Z, Ding J, Shi S. Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis. Acta Pharm Sin B 2023; 13:916-941. [PMID: 36970219 PMCID: PMC10031267 DOI: 10.1016/j.apsb.2022.10.019] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.
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Affiliation(s)
- Mengnan Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Rujing Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Kunmeng Yang
- The First Norman Bethune College of Clinical Medicine, Jilin University, Changchun 130061, China
| | - Yuhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 610031, China
| | - Yachen Peng
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
- Department of Orthopedics, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yuke Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Zhen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jianxun Ding
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Sanjun Shi
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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Gan Y, Zhou M, Ma H, Gong J, Fung SY, Huang X, Yang H. Silver nano-reporter enables simple and ultrasensitive profiling of microRNAs on a nanoflower-like microelectrode array on glass. J Nanobiotechnology 2022; 20:456. [PMID: 36274120 PMCID: PMC9590124 DOI: 10.1186/s12951-022-01664-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractMicroRNAs (miRNAs) are small non-coding RNAs with ~ 22 nucleotides, playing important roles in the post-transcriptional regulation of gene expression. The expression profiles of many miRNAs are closely related to the occurrence and progression of cancer and can be used as biomarkers for cancer diagnosis and prognosis. However, their intrinsic properties, such as short length, low abundance and high sequence homology, represent great challenges in miRNA detection of clinical samples. To overcome these challenges, we developed a simple, ultrasensitive detection platform of electrochemical miRNAs chip (e-miRchip) with a novel signal amplification strategy using silver nanoparticle reporters (AgNRs) for multiplexed, direct, electronic profiling of miRNAs. A two-step hybridization strategy was used to detect miRNAs, where the target miRNA hybridizes with a stem-loop probe to unlock the probe first, and the opened stem-loop can further hybridize with AgNRs for signaling amplification. To enhance the detection sensitivity, the gold nanoflower electrodes (GNEs) were constructed in the microaperture arrays of the e-miRchips by electroplating. With the optimal size of the GNEs, the e-miRchip showed excellent performance for miR-21 detection with a detection limit of 0.56 fM and a linear range extended from 1 fM to 10 pM. The e-miRchip also exhibited good specificity in differentiating the 3-base mismatched sequences of the target miRNA. In addition, the e-miRchip was able to directly detect miR-21 expression in the total RNA extracts or cell lysates collected from lung cancer cells and normal cells. This work demonstrated the developed e-miRchip as an efficient and promising miniaturized point-of-care diagnostic device for the early diagnosis and prognosis of cancers.
Graphical Abstract
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7
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李 帅, 斯 海, 沈 彬. [Application of tetrahedral framework nucleic acids in the treatment of osteoarthritis]. ZHONGGUO XIU FU CHONG JIAN WAI KE ZA ZHI = ZHONGGUO XIUFU CHONGJIAN WAIKE ZAZHI = CHINESE JOURNAL OF REPARATIVE AND RECONSTRUCTIVE SURGERY 2022; 36:505-510. [PMID: 35426293 PMCID: PMC9011070 DOI: 10.7507/1002-1892.202112054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 01/24/2023]
Abstract
Objective To introduce the characteristics of tetrahedral framework nucleic acids (tFNA), focusing on its application in the treatment of osteoarthritis (OA) and relationship with microRNA (miRNA), and prospect the application of tFNA in the treatment of OA and the new idea of constructing miR-tFNA functional complex to treat OA. Methods Recent studies were extensively reviewed to analyze the mechanism of tFNA and its relationship with OA and miRNA. Results tFNA, a new type of new carrier, can not only play an indirect role in the treatment of OA as a small molecular carrier with therapeutic effect, but also play a direct role through the regulation of chondrocytes. It can bind with the miRNA that can regulate OA. The therapeutic effect of constructing tFNA functional complex loaded with miRNA has been verified in various diseases, and tFNA has advantages compared with other vectors. Conclusion tFNA, a novel framework nucleic acid structure, plays an important role in the treatment of OA. Constructing miR-tFNA functional complex may be an innovative idea in the treatment of OA.
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Affiliation(s)
- 帅 李
- 四川大学华西医院骨科研究所 骨科(成都 610041)Orthopedic Research Institute, Department of Orthopedics, West China Hospital, Sichuan University, Chengdu Sichuan, 610041, P. R. China
| | - 海波 斯
- 四川大学华西医院骨科研究所 骨科(成都 610041)Orthopedic Research Institute, Department of Orthopedics, West China Hospital, Sichuan University, Chengdu Sichuan, 610041, P. R. China
| | - 彬 沈
- 四川大学华西医院骨科研究所 骨科(成都 610041)Orthopedic Research Institute, Department of Orthopedics, West China Hospital, Sichuan University, Chengdu Sichuan, 610041, P. R. China
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8
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Li Y, Guo R, Deng C, Li D, Wu H. A Prussian blue nanoparticles-based fluorescent nanoprobe for monitoring microRNA-92a and microRNA-21. ANAL SCI 2022; 38:497-504. [PMID: 35359267 DOI: 10.2116/analsci.20p455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/05/2021] [Indexed: 11/23/2022]
Abstract
Since microRNA-92a (miR-92a) and microRNA-21 (miR-21) are crucial biomarkers for colorectal cancer (CRC), monitoring miR-92a and miR-21 in serum is very significant for the early diagnosis of CRC. In this work, we developed a simple and sensitive fluorescent biosensor for the detection of miR-92a and miR-21 based on the quenching ability of Prussian blue nanoparticles (PBNPs) to fluorophores. Carboxyl fluorescein (FAM)-modified ssDNA (P-92a) and Cyanine 5 (Cy5)-modified ssDNA (P-21) were completely complementary to miR-92a and miR-21 separately. They were adsorbed on PBNPs surface by the binding of PO43- in DNA and Fe3+ in PBNPs to fabricate the P-92a + P-21@PBNPs sensing system. The fluorescence responses from P-92a + P-21@PBNPs show good selection to miR-92a and a great linear process with the miR-92a concentration ranging from 1 to 30 nM (ΔF = 10.978 cmiR-92a + 71.457). Meanwhile, the fluorescence responses from P-92a + P-21@PBNPs is linearly relative to miR-21 from 3 to 30 nM; the linear equation is ΔF = 5.7560 cmiR-21 + 48.729. Furthermore, the detections of miR-92a and miR-21 added in serum samples were achieved. In summary, this method is sensitive, highly specific, time-saving, cost-effective and applicable for the detection of miR-92a and miR-21. Therefore, this present sensor was expected to be used in clinical applications, which lays a potential foundation for an early diagnosis of cancer.
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Affiliation(s)
- Yao Li
- Hunan Provincial Key Laboratory of Micro and Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China
| | - Ren Guo
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Chunyan Deng
- Hunan Provincial Key Laboratory of Micro and Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, People's Republic of China.
| | - Dai Li
- National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Huiyun Wu
- Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, 100850, People's Republic of China
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Sun Y, Yao Y, Wang B, Li Y, Li S, Sui Y, Qiu B. Study on the Biosensor Based on Biomimetic PDA Vesicles Fluorescence Resonance Energy Transfer for the Determination of Ovarian Cancer Marker miRNA-21. ANAL SCI 2021; 37:1349-1353. [PMID: 33431737 DOI: 10.2116/analsci.20p404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In recent years, more and more research is being conducted on microRNAs and their involvement in the regulation of autophagy phagocytosis which is closely related to tumor growth. MicroRNA-21 is a kind of small RNA that can regulate gene expression and plays a significant role in autophagy of tumor cells. But the detection of microRNAs had always been a problem in the field of biological analysis. In this study, we designed a new fluorescent sensor for the detection of miRNA-21. The sensor was based on the successful signal reporting by E36-encapsulated vesicles and the specific interaction between E36 and miRNA-21. In the presence of miRNA, the E36/miRNA-21 complex formed and served as a donor molecule inside the acceptor PDA vesicles to amplify the fluorescence through FRET. Additionally, the sensor was applied to detect miRNA-21 in complex biological samples with satisfactory results.
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Affiliation(s)
- Yang Sun
- Department of Gynecology, Fujian Cancer Hospital, Affiliated Cancer Hospital of Fujian Medical University
| | - Yusheng Yao
- Department of Anesthesiology, Shengli Clinical Medical College of Fujian Medical University &Fujian Provincial Hospital
| | - Bingrong Wang
- Department of Gynecology, Fujian Cancer Hospital, Affiliated Cancer Hospital of Fujian Medical University
| | - Yiying Li
- Department of Gynecology, Fujian Cancer Hospital, Affiliated Cancer Hospital of Fujian Medical University
| | - Siming Li
- Department of Gynecology, Fujian Cancer Hospital, Affiliated Cancer Hospital of Fujian Medical University
| | - Yuxia Sui
- Department of Pharmacy, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital
| | - Bin Qiu
- Ministry of Education Key Laboratory for Analytical Science of Food Safety and Biology, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University
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The biological applications of DNA nanomaterials: current challenges and future directions. Signal Transduct Target Ther 2021; 6:351. [PMID: 34620843 PMCID: PMC8497566 DOI: 10.1038/s41392-021-00727-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/24/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023] Open
Abstract
DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.
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Dong H, Song G, Ma D, Wang T, Jing S, Yang H, Tao Y, Tang Y, Shi Y, Dai Z, Zhu JM, Liu T, Wang B, Leng X, Shen X, Zhu C, Zhao Y. Improved Antiviral Activity of Classical Swine Fever Virus-Targeted siRNA by Tetrahedral Framework Nucleic Acid-Enhanced Delivery. ACS APPLIED MATERIALS & INTERFACES 2021; 13:29416-29423. [PMID: 34148345 DOI: 10.1021/acsami.1c08143] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
DNA self-assembled nanostructures have been considered as effective vehicles for biomolecule delivery because of their excellent biocompatibility, cellular permeability, noncytotoxicity, and small size. Here, we report an efficient antiviral strategy with self-assembled tetrahedral framework nucleic acids (tFNAs) delivering small interfering RNA (t-siRNA) to silence classical swine fever virus (CSFV) gene in porcine host cells. In this study, two previously reported siRNAs, C3 and C6, specifically targeting the CSFV genome were selected and modified on tFNAs, respectively, and termed t-C3 and t-C6. Results indicate that t-C3 and t-C6 can inhibit the viral proliferation of CSFV in kidney derived porcine cells, PK-15, effectively and that inhibition was markedly stronger than free siRNA-C3 or siRNA-C6 only. In addition, the DNA nanostructure also has high cargo-carrying capacity, allowing to deliver multiple functional groups. To improve the antiviral ability of tFNAs, a dual-targeting DNA nanostructure t-C3-C6 was constructed and used to silence the CSFV gene in porcine host cells. This study found that t-C3-C6 can inhibit the viral release and replication, exhibiting outstanding anti-CSFV capabilities. Therefore, these dual-targeting tFNAs have great potential in virus therapy. This strategy not only provides a novel method to inhibit CSFV replication in porcine cells but also verifies that tFNAs are effective tools for delivery of antiviral elements, which have great application potential.
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Affiliation(s)
- Haisi Dong
- Clinical Medical College, Jilin Ginseng Academy, the Affiliated Hospital to Changchun University of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Guangqi Song
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Liver Diseases, Shanghai 200001, China
| | - Danhui Ma
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Liver Diseases, Shanghai 200001, China
| | - Tiedong Wang
- College of Animal Science, School of Pharmacy, Jilin University, Changchun 130012, China
| | - Shisong Jing
- College of Animal Science, School of Pharmacy, Jilin University, Changchun 130012, China
| | - Haimiao Yang
- Clinical Medical College, Jilin Ginseng Academy, the Affiliated Hospital to Changchun University of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Ye Tao
- Clinical Medical College, Jilin Ginseng Academy, the Affiliated Hospital to Changchun University of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Yong Tang
- Clinical Medical College, Jilin Ginseng Academy, the Affiliated Hospital to Changchun University of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Yan Shi
- College of Animal Science, School of Pharmacy, Jilin University, Changchun 130012, China
| | - Zhen Dai
- Department of Gastroenterology, Hepatology, and Endocrinology, Hannover Medical School, Hannover 30625, Germany
| | - Ji-Min Zhu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Liver Diseases, Shanghai 200001, China
| | - Taotao Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Liver Diseases, Shanghai 200001, China
| | - Bingmei Wang
- Clinical Medical College, Jilin Ginseng Academy, the Affiliated Hospital to Changchun University of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Xiangyang Leng
- Clinical Medical College, Jilin Ginseng Academy, the Affiliated Hospital to Changchun University of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Liver Diseases, Shanghai 200001, China
| | - Changfeng Zhu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Liver Diseases, Shanghai 200001, China
| | - Yicheng Zhao
- Clinical Medical College, Jilin Ginseng Academy, the Affiliated Hospital to Changchun University of Chinese Medicine, Changchun University of Chinese Medicine, Changchun 130117, China
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12
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Electrochemiluminescence biosensor for microRNA determination based on AgNCs@MoS 2 composite with (AuNPs-Semicarbazide)@Cu-MOF as coreaction accelerator. Mikrochim Acta 2021; 188:68. [PMID: 33547602 DOI: 10.1007/s00604-020-04678-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
A novel electrochemiluminescence (ECL) biosensor was fabricated for miRNA-162a detection by using silver nanoclusters/molybdenum disulfide (AgNCs@MoS2) as an ECL material, peroxodisulfate (S2O82-) as a co-reactant, and semicarbazide (Sem) as a co-reaction accelerator. Firstly, hairpin probe Ha modified on AgNCs@MoS2/GCE was unfolded based on its hybridization with target microRNA. Then, the unfolded Ha can further be hybridized with another hairpin DNA of Hb on (AuNPs-semicarbazide)@Cu-MOF, resulting in the release of target microRNA, which further causes a cyclic hybridization. This creates more (AuNPs-semicarbazide)@Cu-MOF on the electrode surface, achieving cyclic hybridization signal amplification. Strikingly, due to the presence of Sem, accelerating the reduction of S2O82- and resulting in the generation of more oxidant intermediates of SO42-, the amount of excited states of Agincreases to further amplify the ECL signal. The biosensor exhibited high sensitivity with a low LOD of 1.067 fM, indicating that the introduction of co-reaction accelerators can provide an effective method for signal amplification. The applicability of this method was assessed by investigating the effect of Pb(II) ion on miRNA-162a expression level in maize seedling leaves. A novel electrochemiluminescence biosensor was fabricated for miRNA-162a detection by using silver nanoclusters/molybdenum disulfide as an ECL material, peroxodisulfate as a co-reactant, and semicarbazide as a co-reaction accelerator.
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13
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El Aamri M, Yammouri G, Mohammadi H, Amine A, Korri-Youssoufi H. Electrochemical Biosensors for Detection of MicroRNA as a Cancer Biomarker: Pros and Cons. BIOSENSORS 2020; 10:E186. [PMID: 33233700 PMCID: PMC7699780 DOI: 10.3390/bios10110186] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022]
Abstract
Cancer is the second most fatal disease in the world and an early diagnosis is important for a successful treatment. Thus, it is necessary to develop fast, sensitive, simple, and inexpensive analytical tools for cancer biomarker detection. MicroRNA (miRNA) is an RNA cancer biomarker where the expression level in body fluid is strongly correlated to cancer. Various biosensors involving the detection of miRNA for cancer diagnosis were developed. The present review offers a comprehensive overview of the recent developments in electrochemical biosensor for miRNA cancer marker detection from 2015 to 2020. The review focuses on the approaches to direct miRNA detection based on the electrochemical signal. It includes a RedOx-labeled probe with different designs, RedOx DNA-intercalating agents, various kinds of RedOx catalysts used to produce a signal response, and finally a free RedOx indicator. Furthermore, the advantages and drawbacks of these approaches are highlighted.
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Affiliation(s)
- Maliana El Aamri
- Laboratory of Process Engineering & Environment, Faculty of Sciences and Techniques, Hassan II, University of Casablanca, B.P.146, Mohammedia 28806, Morocco; (M.E.A.); (G.Y.); (H.M.)
| | - Ghita Yammouri
- Laboratory of Process Engineering & Environment, Faculty of Sciences and Techniques, Hassan II, University of Casablanca, B.P.146, Mohammedia 28806, Morocco; (M.E.A.); (G.Y.); (H.M.)
| | - Hasna Mohammadi
- Laboratory of Process Engineering & Environment, Faculty of Sciences and Techniques, Hassan II, University of Casablanca, B.P.146, Mohammedia 28806, Morocco; (M.E.A.); (G.Y.); (H.M.)
| | - Aziz Amine
- Laboratory of Process Engineering & Environment, Faculty of Sciences and Techniques, Hassan II, University of Casablanca, B.P.146, Mohammedia 28806, Morocco; (M.E.A.); (G.Y.); (H.M.)
| | - Hafsa Korri-Youssoufi
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO), Equipe de Chimie Biorganique et Bioinorganique (ECBB), Bât 420, 2 Rue du Doyen Georges Poitou, 91400 Orsay, France;
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14
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Hou L, Huang Y, Hou W, Yan Y, Liu J, Xia N. Modification-free amperometric biosensor for the detection of wild-type p53 protein based on the in situ formation of silver nanoparticle networks for signal amplification. Int J Biol Macromol 2020; 158:580-586. [PMID: 32380113 DOI: 10.1016/j.ijbiomac.2020.04.271] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/12/2020] [Accepted: 04/30/2020] [Indexed: 02/03/2023]
Abstract
Sensitive and accurate quantification of wild-type p53 protein is of great importance for biological research and clinical diagnosis. Herein, a modification-free amperometric biosensor was proposed for sensitive detection of wild-type p53 protein by the signal amplification of silver nanoparticles (AgNPs) networks formed in situ on electrode surface. Double-stranded DNA (dsDNA) probe containing two consensus sites was immobilized on gold electrode surface to capture wild-type p53 protein. The cysteine thiol and amine groups on the exterior of the protein allowed for the attachment of bare AgNPs through the AgS or AgN interactions. Meanwhile, benzene-1,4-dithiol (BDT) molecules in solution triggered the assembly of more AgNPs on electrode surface through the AgS interactions, thus leading to the in situ formation of AgNPs networks for signal amplification. The target at the concentration as low as 0.1 pM can be readily determined. This method was further applied to determine wild-type p53 protein in spiked human serum and cell lysates with satisfactory results. Moreover, the biosensor is regenerative and does not require the modification of AgNPs with recognition element for signal readout. The modification-free strategy can potentially be applied to develop novel biosensors for detection of other biological macromolecules.
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Affiliation(s)
- Linlin Hou
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Yaliang Huang
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Weilin Hou
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Yurou Yan
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Jinlin Liu
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan 455000, People's Republic of China
| | - Ning Xia
- Henan Province of Key Laboratory of New Optoelectronic Functional Materials, Anyang Normal University, Anyang, Henan 455000, People's Republic of China.
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15
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DNA framework-engineered electrochemical biosensors. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1130-1141. [PMID: 32253588 DOI: 10.1007/s11427-019-1621-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/04/2020] [Indexed: 02/07/2023]
Abstract
Self-assembled DNA nanostructures have shown remarkable potential in the engineering of biosensing interfaces, which can improve the performance of various biosensors. In particular, by exploiting the structural rigidity and programmability of the framework nucleic acids with high precision, molecular recognition on the electrochemical biosensing interface has been significantly enhanced, leading to the development of highly sensitive and specific biosensors for nucleic acids, small molecules, proteins, and cells. In this review, we summarize recent advances in DNA framework-engineered biosensing interfaces and the application of corresponding electrochemical biosensors.
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16
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Sirong S, Yang C, Taoran T, Songhang L, Shiyu L, Yuxin Z, Xiaoru S, Tao Z, Yunfeng L, Xiaoxiao C. Effects of tetrahedral framework nucleic acid/wogonin complexes on osteoarthritis. Bone Res 2020; 8:6. [PMID: 32047705 PMCID: PMC7010777 DOI: 10.1038/s41413-019-0077-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/26/2019] [Accepted: 06/13/2019] [Indexed: 02/05/2023] Open
Abstract
Osteoarthritis, a disorder characterized by articular cartilage deterioration, varying degrees of inflammation, and chondrocyte apoptosis, is the most common chronic joint disease. To slow or reverse its progression, inflammation should be inhibited, and chondrocyte proliferation should be promoted. Tetrahedral framework nucleic acids can be internalized by chondrocytes (even inflammatory chondrocytes) and can enhance their proliferation and migration. Wogonin, a naturally occurring flavonoid, suppresses oxidative stress and inhibits inflammation. In this study, tetrahedral framework nucleic acids were successfully self-assembled and used to load wogonin. We confirmed the effective formation of tetrahedral framework nucleic acid/wogonin complexes by dynamic light scattering, zeta potential analysis, transmission electron microscopy, and fluorescence spectrophotometry. Tetrahedral framework nucleic acids, wogonin, and especially tetrahedral framework nucleic acid/wogonin complexes effectively alleviated inflammation in vitro and in vivo and prevented cartilage destruction. In addition, these materials remarkably downregulated the expression of inflammatory mediators and matrix metalloproteinases, upregulated chondrogenic markers, and promoted tissue inhibitor of metalloproteinase 1 and B-cell lymphoma 2 expression. In vivo, after treatment with tetrahedral framework nucleic acid/wogonin complexes, the bone mineral density in regenerated tissues was much higher than that found in the untreated groups. Histologically, the complexes enhanced new tissue regeneration, significantly suppressed chondrocyte apoptosis, and promoted chondrogenic marker expression. They also inhibited cell apoptosis, increased chondrogenic marker expression, and suppressed the expression of inflammatory mediators in osteoarthritis. Therefore, we believe that tetrahedral framework nucleic acid/wogonin complexes can be used as an injectable form of therapy for osteoarthritis.
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Affiliation(s)
- Shi Sirong
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Chen Yang
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, 610041 Sichuan Province China
| | - Tian Taoran
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Li Songhang
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Lin Shiyu
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Zhang Yuxin
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Shao Xiaoru
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Zhang Tao
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Lin Yunfeng
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
| | - Cai Xiaoxiao
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hosptial of Stomatology, Sichuan University, Chengdu, 610041 China
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17
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Wang X, Wu J, Mao W, He X, Ruan L, Zhu J, Shu P, Zhang Z, Jiang B, Zhang X. A tetrahedral DNA nanostructure-decorated electrochemical platform for simple and ultrasensitive EGFR genotyping of plasma ctDNA. Analyst 2020; 145:4671-4679. [PMID: 32458862 DOI: 10.1039/d0an00591f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In this study, we propose an on-site electrochemical platform for sensitive simultaneous genotyping of the two major EGFR mutations (19del and L858R) through plasma ctDNA based on tetrahedral DNA nanostructure decorated screen-printed electrodes.
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18
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Li Y, Zhai Y, Liu W, Zhang K, Liu J, Shi J, Zhang Z. Ultrasmall nanostructured drug based pH-sensitive liposome for effective treatment of drug-resistant tumor. J Nanobiotechnology 2019; 17:117. [PMID: 31783863 PMCID: PMC6884872 DOI: 10.1186/s12951-019-0550-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/18/2019] [Indexed: 02/04/2023] Open
Abstract
Background Cancer cells always develop ways to resist and evade chemotherapy. To overcome this obstacle, herein, we introduce a programmatic release drug delivery system that imparts avoiding drug efflux and nuclear transport in synchrony via a simple nanostructured drug strategy. Results The programmatic liposome-based nanostructured drugs (LNSD) contained two modules: doxorubicin (DOX) loaded into tetrahedral DNA (TD, ~ 10 nm) to form small nanostructured DOX, and the nanostructured DOX was encapsulated into the pH-sensitive liposomes. In the in vitro and in vivo studies, LNSD shows multiple benefits for drug resistance tumor treatment: (1) not only enhanced the cellular DOX uptake, but also maintained DOX concentration in an optimum level in resistant tumor cells via nanostructure induced anti-efflux effect; (2) small nanostructured DOX efficiently entered into cell nuclear via size depended nuclear-transport for enhanced treatment; (3) improved the pharmacokinetics and biodistribution via reducing DOX leakage during circulation. Conclusions The system developed in this study has the potential to provide new therapies for drug-resistant tumor.
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Affiliation(s)
- Yanyan Li
- The Fifth Affiliated Hospital of Zhengzhou University, Kangfu Road, Zhengzhou, 450052, China
| | - Yongxia Zhai
- The Fifth Affiliated Hospital of Zhengzhou University, Kangfu Road, Zhengzhou, 450052, China
| | - Wei Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China. .,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou, Henan, China. .,Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, Henan, China.
| | - Junjie Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China. .,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou, Henan, China. .,Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, Henan, China.
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China. .,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou, Henan, China. .,Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, Henan, China.
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou, Henan, China.,Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou, Henan, China
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19
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Hahn J, Shih WM. Thermal cycling of DNA devices via associative strand displacement. Nucleic Acids Res 2019; 47:10968-10975. [PMID: 31584082 PMCID: PMC6847259 DOI: 10.1093/nar/gkz844] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 12/23/2022] Open
Abstract
DNA-based devices often operate through a series of toehold-mediated strand-displacement reactions. To achieve cycling, fluidic mixing can be used to introduce 'recovery' strands to reset the system. However, such mixing can be cumbersome, non-robust, and wasteful of materials. Here we demonstrate mixing-free thermal cycling of DNA devices that operate through associative strand-displacement cascades. These cascades are favored at low temperatures due to the primacy of a net increase in base pairing, whereas rebinding of 'recovery' strands is favored at higher temperatures due to the primacy of a net release of strands. The temperature responses of the devices could be modulated by adjustment of design parameters such as the net increase of base pairs and the concentrations of strands. Degradation of function was not observable even after 500 thermal cycles. We experimentally demonstrated simple digital-logic circuits that evaluate at 35°C and reset after transient heating to 65°C. Thus associative strand displacement enables robust thermal cycling of DNA-based devices in a closed system.
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Affiliation(s)
- Jaeseung Hahn
- Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA.,Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA.,Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - William M Shih
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA.,Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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20
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Chandrasekaran AR, Punnoose JA, Zhou L, Dey P, Dey BK, Halvorsen K. DNA nanotechnology approaches for microRNA detection and diagnosis. Nucleic Acids Res 2019; 47:10489-10505. [PMID: 31287874 PMCID: PMC6847506 DOI: 10.1093/nar/gkz580] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.
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Affiliation(s)
| | | | - Lifeng Zhou
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
| | - Paromita Dey
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
| | - Bijan K Dey
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
- Department of Biological Sciences, University at Albany, State University of New York, NY 12222, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, NY 12222, USA
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21
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Carter MLJ, Rusling DA, Gurr S, Brown T, Fox KR. Stability of the different arms of a DNA tetrahedron and its interaction with a minor groove ligand. Biophys Chem 2019; 256:106270. [PMID: 31706136 DOI: 10.1016/j.bpc.2019.106270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/02/2019] [Accepted: 10/02/2019] [Indexed: 11/27/2022]
Abstract
DNA strands can be designed to assemble into stable three-dimensional structures, based on Watson-Crick base pairing rules. The simplest of these is the DNA tetrahedron that is composed of four oligonucleotides. We have re-designed the sequence of a DNA tetrahedron so that it contains a single (AATT) binding site for the minor groove binding ligand Hoechst 33258. We examined the stability of this structure by placing fluorescent groups within each of its edges and have shown that all the edges melt at the same temperature in the absence of the ligand. The minor groove ligand still binds to its recognition sequence within the tetrahedron and increases the melting temperature of the folded complex. This ligand-induced stabilisation is propagated into the adjacent helical arms and the tetrahedron melts as a single entity in a cooperative fashion.
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Affiliation(s)
- Michael L J Carter
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - David A Rusling
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Steven Gurr
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Keith R Fox
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom.
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22
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Guo X, Li M, Zhao R, Yang Y, Wang R, Wu F, Jia L, Zhang Y, Wang L, Qu Z, Wang F, Zhu Y, Hao R, Zhang X, Song H. Structural and positional impact on DNAzyme-based electrochemical sensors for metal ions. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 21:102035. [DOI: 10.1016/j.nano.2019.102035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/24/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
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23
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Han S, Liu W, Yang S, Wang R. Facile and Label-Free Electrochemical Biosensors for MicroRNA Detection Based on DNA Origami Nanostructures. ACS OMEGA 2019; 4:11025-11031. [PMID: 31460200 PMCID: PMC6649092 DOI: 10.1021/acsomega.9b01166] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/13/2019] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) have emerged as the promising molecular biomarkers for early diagnosis and enhanced understanding of the molecular pathogenesis of cancers as well as certain diseases. Here, a facile, label-free, and amplification-free electrochemical biosensor was developed to detect miRNA by using DNA origami nanostructure-supported DNA probes, with methylene blue (MB) serving as the hybridization redox indicator, for the first time. Specifically, the use of cross-shaped DNA origami nanostructures containing multiple single-stranded DNA probes at preselected locations on each DNA nanostructure could increase the accessibility and the recognition efficiency of the probes (due to the rational controlled density of DNA probes). The successful immobilization of DNA origami probes and their hybridization with targeted miRNA-21 molecules was confirmed by electrochemical impedance spectroscopy and cyclic voltammetry methods. A differential pulse voltammetry technique was employed to record the oxidation peak current of MB before and after target hybridization. The linear detection range of this biosensor was from 0.1 pM to 10.0 nM, with a lower detection limit of 79.8 fM. The selectivity of the miRNA biosensor was also studied by observing the discrimination ability of single-base mismatched sequences. Because of the larger surface area and unprecedented customizability of DNA origami nanostructures, this strategy demonstrated great potential for sensitive, selective, and label-free determination of miRNA for translational biomedical research and clinical applications.
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Affiliation(s)
- Shuo Han
- Department
of Chemistry and Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Wenyan Liu
- Department
of Chemistry and Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Shuo Yang
- Department
of Chemistry and Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Risheng Wang
- Department
of Chemistry and Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
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24
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Chai H, Cheng W, Xu L, Gui H, He J, Miao P. Fabrication of Polymeric Ferrocene Nanoparticles for Electrochemical Aptasensing of Protein with Target-Catalyzed Hairpin Assembly. Anal Chem 2019; 91:9940-9945. [DOI: 10.1021/acs.analchem.9b01673] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hua Chai
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People’s Republic of China
- Jihua Laboratory, Foshan 528200, People’s Republic of China
| | - Wenbo Cheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People’s Republic of China
- Tianjin Guokeyigong Science and Technology Development Co., Ltd., Tianjin 300399, People’s Republic of China
| | - Lei Xu
- College of Chemistry, Chemical Engineering and Materials Science, State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Soochow University, Suzhou 215123, People’s Republic of China
| | - Huiqiang Gui
- College of Chemistry, Chemical Engineering and Materials Science, State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Soochow University, Suzhou 215123, People’s Republic of China
| | - Jinlin He
- College of Chemistry, Chemical Engineering and Materials Science, State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Functional Polymer Design and Application, Soochow University, Suzhou 215123, People’s Republic of China
| | - Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People’s Republic of China
- Jihua Laboratory, Foshan 528200, People’s Republic of China
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25
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Abstract
Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.
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Affiliation(s)
- Hong Zhou
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Jing Liu
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Jing-Juan Xu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China.
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi, China.
| | - Hong-Yuan Chen
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
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26
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Su Y, Li D, Liu B, Xiao M, Wang F, Li L, Zhang X, Pei H. Rational Design of Framework Nucleic Acids for Bioanalytical Applications. Chempluschem 2019; 84:512-523. [DOI: 10.1002/cplu.201900118] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Yuwei Su
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Dan Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Bingyi Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Fei Wang
- Joint Research Center for Precision MedicineShanghai Jiao Tong University & Affiliated Sixth People's Hospital South Campus 6600th Nanfeng Road, Fengxian District Shanghai 201499 P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
| | - Xueli Zhang
- Joint Research Center for Precision MedicineShanghai Jiao Tong University & Affiliated Sixth People's Hospital South Campus 6600th Nanfeng Road, Fengxian District Shanghai 201499 P. R. China
- Southern Medical University Affiliated Fengxian Hospital Shanghai 201499 P. R. China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular EngineeringEast China Normal University 500 Dongchuan Road Shanghai 200241 P.R. China
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Zhan Y, Ma W, Zhang Y, Mao C, Shao X, Xie X, Wang F, Liu X, Li Q, Lin Y. DNA-Based Nanomedicine with Targeting and Enhancement of Therapeutic Efficacy of Breast Cancer Cells. ACS APPLIED MATERIALS & INTERFACES 2019; 11:15354-15365. [PMID: 30924334 DOI: 10.1021/acsami.9b03449] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recently, a DNA tetrahedron has been reported to be a novel nanomedicine and promising drug vector because of its compactness, biocompatibility, biosafety, and editability. Here, we modified the DNA tetrahedron with a DNA aptamer (AS1411) as a DNA-based delivery system, which could bind to nucleolin for its cancer cell selectivity. Nucleolin is a specific biomarker protein overexpressed on membranes of malignant cancer cells and its deregulation is implicated in cell proliferation. The antimetabolite drug 5-fluorouracil (5-FU) is an extensively used anticancer agent; however, its major limitation is the lack of target specificity. Cyanine 5 (Cy5), a fluorescent probe, can be used to label DNA tetrahedron and enhance photostability with minimal effects on its basic functions. In this study, we additionally attached 5-FU to the DNA-based delivery system as a new tumor-targeting nanomedicine (AS1411-T-5-FU) to enhance the therapeutic efficacy and targeting of breast cancer. We examined the difference of the cellular uptake of AS1411-T-5-FU between breast cancer cells and normal breast cells and concluded that AS1411-T-5-FU had a better targeting ability to kill breast cancer cells than 5-FU. We further evaluated the expressions of cell apoptosis-related proteins and genes, which are associated with the mitochondrial apoptotic pathway. Ultimately, our results suggest the potential of DNA tetrahedron in cancer therapies, and we develop a novel approach to endow 5-FU with targeting property.
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Affiliation(s)
- Yuxi Zhan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Chenchen Mao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Xiaoru Shao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Xueping Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Fei Wang
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Qian Li
- School of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
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28
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Cao Y, Dai Y, Chen H, Tang Y, Chen X, Wang Y, Zhao J, Zhu X. Integration of fluorescence imaging and electrochemical biosensing for both qualitative location and quantitative detection of cancer cells. Biosens Bioelectron 2019; 130:132-138. [PMID: 30735946 DOI: 10.1016/j.bios.2019.01.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/09/2019] [Accepted: 01/17/2019] [Indexed: 12/16/2022]
Abstract
In this work, DNA-templated silver nanoclusters (DNA-AgNCs) with unique fluorescent and electrochemical properties are prepared as dual signal probes for both qualitative imaging and quantitative detection of cancer cells in an integrated system. ITO electrode that has good light transmittance and electric conductivity is employed as a substrate for dual analysis of cancer cells. ITO electrode is firstly modified by AS1141 aptamer, which could selectively bind to nucleolin overexpressed on the surface of a model breast cancer cell, MCF-7 cell line. The composite of mucin 1 antibody (anti-MUC1) and DNA-AgNCs then binds to MUC1 on the surface of captured MCF-7 cell, forming a sandwich-like structure. Therefore, our method allows noninvasive fluorescence imaging and amplified electrochemical detection using a single labeling platform, providing a biocompatible and highly specific method for adequate analysis of cancer cells. Experimental results demonstrate that strong red fluorescence of DNA-AgNCs clearly displays the loading of cancer cells on ITO electrode after dual recognition, and amplified electrochemical signals of DNA-AgNCs enable improved sensitivity toward quantitative analysis with a detection limit of 3 cells.
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Affiliation(s)
- Ya Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Yuhao Dai
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Hong Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Yingying Tang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Xu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Ying Wang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China.
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China.
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Abstract
High-throughput profiling/sensing of nucleic acids has recently emerged as a highly promising strategy for the early diagnosis and improved prognosis of a broad range of pathologies, most notably cancer. Among the potential biomarker candidates, microRNAs (miRNAs), a class of non-coding RNAs of 19-25 nucleotides in length, are of particular interest due to their role in the post-transcriptional regulation of gene expression. Developing miRNA sensing technologies that are quantitative, ultrasensitive and highly specific has proven very challenging because of their small size, low natural abundance and the high degree of sequence similarity among family members. When compared to optical based methods, electrochemical sensors offer many advantages in terms of sensitivity and scalability. This non-comprehensive review aims to break-down and highlight some of the most promising strategies for electrochemical sensing of microRNA biomarkers.
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Affiliation(s)
- Philip Gillespie
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
| | - Danny O'Hare
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
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30
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Ma W, Xie X, Shao X, Zhang Y, Mao C, Zhan Y, Zhao D, Liu M, Li Q, Lin Y. Tetrahedral DNA nanostructures facilitate neural stem cell migration via activating RHOA/ROCK2 signalling pathway. Cell Prolif 2018; 51:e12503. [PMID: 30091500 DOI: 10.1111/cpr.12503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 06/20/2018] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES The main purpose of current study was to explore the effects of tetrahedral DNA nanostructures (TDNs) on neuroectodermal (NE-4C) stem cells migration and unveil the potential mechanisms. MATERIALS AND METHODS The successfully self-assembled TDNs were also determined by dynamic light scattering (DLS). A bidirectional wound-healing assay and transwell chamber assay were employed to test the migrating behaviour of NE-4C stem cells cultured under different conditions. RESULTS Through an in vitro study, we found that stem cells could internalize TDNs quickly, and the cells' parallel and vertical migration was promoted effectively. Besides, the effects of TDNs were found being exerted by upregulating the gene and protein expression levels of RhoA, Rock2 and Vinculin, indicating that the RHOA/ROCK2 pathway was activated by the TDNs during the cell migration. CONCLUSIONS In conclusion, TDNs could enter NSCs without the aid of other transfection reagents in large amounts, whereas only small amounts of ssDNA could enter the cells. TDNs taken up by NSCs activated the RHOA/ROCK2 signalling pathway, which had effects on the relevant genes and proteins expression, eventually promoting the migration of NE-4C stem cells. These findings suggested that TDNs have great potential in application for the repair and regeneration of neural tissue.
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Affiliation(s)
- Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xueping Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaoru Shao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenchen Mao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuxi Zhan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dan Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mengting Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qianshun Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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31
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Shiu SCC, Fraser LA, Ding Y, Tanner JA. Aptamer Display on Diverse DNA Polyhedron Supports. Molecules 2018; 23:E1695. [PMID: 29997372 PMCID: PMC6099927 DOI: 10.3390/molecules23071695] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 11/19/2022] Open
Abstract
DNA aptamers are important tools for molecular recognition, particularly for a new generation of tools for biomedicine based on nucleic acid nanostructures. Here, we investigated the relative abilities of different shapes and sizes of DNA polyhedra to display an aptamer which binds to the malaria biomarker Plasmodium falciparum lactate dehydrogenase (PfLDH). The aptamer was shown to perform an Aptamer-Tethered Enzyme Capture (APTEC) assay with the hypothesis that the display of the aptamer above the surface through the use of a polyhedron may lead to better sensitivity than use of the aptamer alone. We compared different numbers of points of contact, different shapes, including tetrahedron, square, and pentagon-based pyramids, as well as prisms. We also investigated the optimal height of display of the structure. Our results demonstrated that the display of an aptamer on an optimized nanostructure improved sensitivity up to 6-fold relative to the aptamer alone in the APTEC assay. Other important factors included multiple basal points of contact with the surface, a tetrahedron proved superior to the more complex shaped structures, and height above the surface only made minor differences to efficacy. The display of an aptamer on a nanostructure may be beneficial for higher sensitivity aptamer-mediated malaria diagnosis. Aptamer displays using DNA nanostructure polyhedron supports could be a useful approach in a variety of applications.
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Affiliation(s)
- Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Lewis A Fraser
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Yifan Ding
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
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32
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Abstract
Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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33
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Harroun SG, Prévost-Tremblay C, Lauzon D, Desrosiers A, Wang X, Pedro L, Vallée-Bélisle A. Programmable DNA switches and their applications. NANOSCALE 2018; 10:4607-4641. [PMID: 29465723 DOI: 10.1039/c7nr07348h] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.
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Affiliation(s)
- Scott G Harroun
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada.
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34
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Ma W, Shao X, Zhao D, Li Q, Liu M, Zhou T, Xie X, Mao C, Zhang Y, Lin Y. Self-Assembled Tetrahedral DNA Nanostructures Promote Neural Stem Cell Proliferation and Neuronal Differentiation. ACS APPLIED MATERIALS & INTERFACES 2018; 10:7892-7900. [PMID: 29424522 DOI: 10.1021/acsami.8b00833] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Stem cell-based therapy is considered a promising approach for the repair of nervous tissues. Neural stem cells (NSCs) cannot proliferate or differentiate efficiently; hence, different biomaterials have been explored to improve NSC proliferation and differentiation. However, these agents either had low bioavailability or poor biocompatibility. In this work, our group investigated the effects of tetrahedral DNA nanostructures (TDNs), a novel DNA biological material, on the self-renew and differentiation of neuroectodermal (NE-4C) stem cells. We observed that TDN treatment promoted self-renew of the stem cells via activating the Wnt/β -catenin pathway. In addition, our findings suggested that NE-4C stem cells' neuronal differentiation could be promoted effectively by TDNs via inhibiting the notch signaling pathway. In summary, this is the first report about the effects of TDNs on the proliferation and differentiation of NE-4C stem cells and the results demonstrate that TDNs have a great potential in nerve tissue regeneration.
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Affiliation(s)
- Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Xiaoru Shao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Dan Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Qianshun Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Mengting Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Tengfei Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Xueping Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Chenchen Mao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Yuxin Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology , Sichuan University , Chengdu 610041 , P. R. China
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35
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Bo B, Zhang T, Jiang Y, Cui H, Miao P. Triple Signal Amplification Strategy for Ultrasensitive Determination of miRNA Based on Duplex Specific Nuclease and Bridge DNA–Gold Nanoparticles. Anal Chem 2018; 90:2395-2400. [PMID: 29308636 DOI: 10.1021/acs.analchem.7b05447] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bing Bo
- Shanghai
Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433 P. R. China
| | - Tian Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 P. R. China
| | - Yiting Jiang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 P. R. China
| | - Haiyan Cui
- Shanghai
Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433 P. R. China
| | - Peng Miao
- Shanghai
Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433 P. R. China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 P. R. China
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36
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Li Q, Zhao D, Shao X, Lin S, Xie X, Liu M, Ma W, Shi S, Lin Y. Aptamer-Modified Tetrahedral DNA Nanostructure for Tumor-Targeted Drug Delivery. ACS APPLIED MATERIALS & INTERFACES 2017; 9:36695-36701. [PMID: 28991436 DOI: 10.1021/acsami.7b13328] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Tetrahedral DNA nanostructures (TDNs) are considered promising drug delivery carriers because they are able to permeate cellular membrane and are biocompatible and biodegradable. Furthermore, they can be modified by functional groups. To improve the drug-delivering ability of TDNs, we chose anticancer aptamer AS1411 to modify TDNs for tumor-targeted drug delivery. AS1411 can specifically bind to nucleolin, which is overexpressed on the cell membrane of tumor cells. Furthermore, AS1411 can inhibit NF-κB signaling and reduce the expression of bcl-2. In this study, we compared the intracellular localization of AS1411-modified TDNs (Apt-TDNs) with that of TDNs in different cells under hypoxic condition. Furthermore, we compared the effects of Apt-TDNs and TDNs on cell growth and cell cycle under hypoxic condition. A substantial amount of Apt-TDNs entered and accumulated in the nucleus of MCF-7 cells; however, the amount of Apt-TDNs that entered L929 cells was comparatively less. TDNs entered in much lower quantity in MCF-7 cells than Apt-TDNs. Moreover, there was little difference in the amount of TDNs that entered L929 cells and MCF-7 cells. Apt-TDNs can inhibit MCF-7 cell growth and promote L929 cell growth, while TDNs can promote both MCF-7 and L929 cell growth. Thus, the results indicate that Apt-TDNs are more effective tumor-targeted drug delivery vehicles than TDNs, with the ability to specifically inhibit tumor cell growth.
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Affiliation(s)
- Qianshun Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
| | - Dan Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
| | - Xiaoru Shao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
| | - Shiyu Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
| | - Xueping Xie
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
| | - Mengting Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
| | - Wenjuan Ma
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University , Chengdu 610041, PR China
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37
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Wang J, Cheng W, Meng F, Yang M, Pan Y, Miao P. Hand-in-hand RNA nanowire-based aptasensor for the detection of theophylline. Biosens Bioelectron 2017; 101:153-158. [PMID: 29065340 DOI: 10.1016/j.bios.2017.10.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/08/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022]
Abstract
Theophylline is a popular drug for many respiratory diseases. However, certain toxic side effects may be developed and the narrow safety range raises the demand for sensitive methods to constantly monitor theophylline levels. This study presents an electrochemical approach towards theophylline detection based on the recognition by split RNA aptamers. Target induced construction of hand-in-hand RNA nanowire on the electrode surface could further absorb silver nanoparticles (Ag NPs) as electrochemical species. When theophylline is not present, RNA probes are stable and their conformations remain unchanged. In contrast, theophylline is able to trigger the hairpin opening of RNA probe and subsequent self-assembly of RNA nanowire, which could be captured by DNA tetrahedron on the electrode interface. After further decorating Ag NPs on the nanowire, silver stripping current is measured to reveal initial theophylline concentration. The developed sensing strategy shows excellent specificity and sensitivity with the limit of detection of 50nM. Its practical utility is demonstrated by quantitative determination of theophylline levels in complex biological samples.
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Affiliation(s)
- Jue Wang
- Department of Neurology, Shanghai Tenth People's Hospital Tongji University School of Medicine, Shanghai 200072, PR China
| | - Wenbo Cheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China
| | - Fanyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China
| | - Mo Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, PR China
| | - Yue Pan
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, PR China.
| | - Peng Miao
- Department of Neurology, Shanghai Tenth People's Hospital Tongji University School of Medicine, Shanghai 200072, PR China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
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38
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Liang L, Lan F, Yin X, Ge S, Yu J, Yan M. Metal-enhanced fluorescence/visual bimodal platform for multiplexed ultrasensitive detection of microRNA with reusable paper analytical devices. Biosens Bioelectron 2017; 95:181-188. [DOI: 10.1016/j.bios.2017.04.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 04/02/2017] [Accepted: 04/20/2017] [Indexed: 01/20/2023]
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39
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Qi L, Xiao M, Wang X, Wang C, Wang L, Song S, Qu X, Li L, Shi J, Pei H. DNA-Encoded Raman-Active Anisotropic Nanoparticles for microRNA Detection. Anal Chem 2017; 89:9850-9856. [DOI: 10.1021/acs.analchem.7b01861] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lin Qi
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Mingshu Xiao
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Xiwei Wang
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Cheng Wang
- Department
of Nuclear Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P. R. China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China
| | - Xiangmeng Qu
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Jiye Shi
- Kellogg
College, University of Oxford, Oxford OX2 6PN, U.K
| | - Hao Pei
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes, School of
Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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Shi S, Lin S, Shao X, Li Q, Tao Z, Lin Y. Modulation of chondrocyte motility by tetrahedral DNA nanostructures. Cell Prolif 2017; 50. [PMID: 28792637 DOI: 10.1111/cpr.12368] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/05/2017] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Contemporarily, a highly increasing attention was paid to nanoconstructs, particularly DNA nanostructures possessing precise organization, functional manipulation, biocompatibility and biodegradability. Amongst these DNA nanomaterials, tetrahedral DNA nanostructures (TDNs) are a significantly ideal bionanomaterials with focusing on the property that can be internalized into cytoplasm in the absence of transfection. Therefore, the focus of this study was on investigating the influence of TDNs on the chondrocytes locomotion. MATERIALS AND METHODS Tetrahedral DNA nanostructures was confirmed by 6% polyacrylamide gel electrophoresis (PAGE) and dynamic light scattering (DLS). Subsequently, the effect of TDNs on chondrocyte locomotion was investigated by real-time cell analysis (RTCA) and wound healing assay. The variation of relevant genes and proteins was detected by quantitative polymerase chain reaction (qPCR), western blotting and immunofluorescence respectively. RESULTS We demonstrated that tetrahedral DNA nanostructures have positive influence on chondrocytes locomotion and promoted the expression of RhoA, ROCK2 and vinculin. Additionally, upon exposure to TDNs with the concentration of 250 nmol L-1 , the chondrocytes were showed the highest motility via both RTCA and wound healing assay. Meanwhile, the mRNA and protein expression of RhoA, ROCK2 and vinculin were also significantly enhanced with the same concentration. CONCLUSIONS It can be concluded that the TDNs with the optimal concentration of 250 nmol L-1 could extremely promoted the chondrocytes locomotion through facilitating the expression of RhoA, ROCK2 and vinculin. These results seemed to reveal that this special three-dimensional DNA tetrahedral nanostructures may be applied to cartilage repair and treatment in the future.
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Affiliation(s)
- Sirong Shi
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Shiyu Lin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoru Shao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Qianshun Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Zhang Tao
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
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Liu L, Chang Y, Xia N, Peng P, Zhang L, Jiang M, Zhang J, Liu L. Simple, sensitive and label–free electrochemical detection of microRNAs based on the in situ formation of silver nanoparticles aggregates for signal amplification. Biosens Bioelectron 2017; 94:235-242. [DOI: 10.1016/j.bios.2017.02.041] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 02/15/2017] [Accepted: 02/23/2017] [Indexed: 01/25/2023]
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42
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Tao Y, Yin D, Jin M, Fang J, Dai T, Li Y, Li Y, Pu Q, Xie G. Double-loop hairpin probe and doxorubicin-loaded gold nanoparticles for the ultrasensitive electrochemical sensing of microRNA. Biosens Bioelectron 2017; 96:99-105. [PMID: 28475957 DOI: 10.1016/j.bios.2017.04.040] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/31/2017] [Accepted: 04/25/2017] [Indexed: 12/15/2022]
Abstract
An electrochemical microRNA (miRNA) analysis platform by combining double-loop hairpin probe (DHP) and doxorubicin-loaded gold nanoparticles (AuNPs@Dox) for ultrasensitive miRNA detection is proposed. Firstly, we here report a DHP that is simultaneously engineered to incorporate a miRNA recognition sequence, an output segment and output's complementary fragment. The important aspect of this hairpin probe is that it would not be degraded by duplex specific nuclease (DSN) and circumvents elaborately chemical modification disadvantages encountered by classic molecular beacon. For the DHP-based DSN signal amplification system, DHP hybridizes with target miRNA to form DNA-miRNA heteroduplexes, and the DSN can hydrolyze the DNA in the heteroduplexes structure selectively, while released target miRNA strand can initiate another cycle resulting in a significant signal amplification and the accumulated output segments could be responsible for strand displacement on the electrode directly. Furthermore, a great deal of doxorubicin (Dox) are loaded on the gold nanoparticles (AuNPs) to fabricate the AuNPs@Dox biocomposites that could magnify the electrochemical signal and enable the ultrasensitive analysis of miRNA. As a result, the miRNA was capable of being detected in a limit of 0.17pM and other kinds of miRNA were discriminated facilely by this method. The described DHP as a toolbox and the nano-biocomposites as a novel signal material would not only promote the design of electrochemical biosensors but also open a good way to promote the establishment of test method in malignant tumors.
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Affiliation(s)
- Yiyi Tao
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Dan Yin
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Mingchao Jin
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Jie Fang
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Tao Dai
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yi Li
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yuxia Li
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China
| | - Qinli Pu
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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Amperometric biosensor for microRNA based on the use of tetrahedral DNA nanostructure probes and guanine nanowire amplification. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2246-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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44
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Campuzano S, Yánez-Sedeño P, Pingarrón JM. Electrochemical biosensing of microribonucleic acids using antibodies and viral proteins with affinity for ribonucleic acid duplexes. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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45
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Li J, Li D, Yuan R, Xiang Y. Biodegradable MnO 2 Nanosheet-Mediated Signal Amplification in Living Cells Enables Sensitive Detection of Down-Regulated Intracellular MicroRNA. ACS APPLIED MATERIALS & INTERFACES 2017; 9:5717-5724. [PMID: 28124559 DOI: 10.1021/acsami.6b13073] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The monitoring of intracellular microRNAs plays important roles in elucidating the biological function and biogenesis of miRNAs in living cells. However, because of their sequence similarity, low abundance, and small size, it is a great challenge to detect intracellular miRNAs, especially for those with much lower expression levels. To address this issue, we have developed an in cell signal amplification approach for monitoring down-regulated miRNAs in living cells based on biodegradable MnO2 nanosheet-mediated and target-triggered assembly of hairpins. The MnO2 nanosheets can adsorb and exhibit an excellent quenching effect to the dye labeled hairpin probes. Besides, due to their biodegradability, the MnO2 nanosheets feature highly reduced cytotoxicity to the target cells. Upon entering cells, the surface-adsorbed FAM- and Tamra (TMR)-conjugated hairpins can be released due to the displacement reactions by other proteins or nucleic acids and the degradation of the MnO2 nanosheets by cellular GSH. Subsequently, the down-regulated target miRNA-21 triggers cascaded assembly of the two hairpins into long dsDNA polymers, which brings the fluorescence resonance energy transfer (FRET) pair, FAM (donor), and TMR (acceptor) into close proximity to generate significantly enhanced FRET signals for detecting trace miRNA-21 in living cells. By carefully tailoring the sequences of the hairpins, the developed method can offer new opportunities for monitoring various trace intracellular miRNA targets with low expression levels in living cells.
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Affiliation(s)
- Jing Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Daxiu Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University , Chongqing 400715, P. R. China
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Xie N, Liu S, Yang X, He X, Huang J, Wang K. DNA tetrahedron nanostructures for biological applications: biosensors and drug delivery. Analyst 2017; 142:3322-3332. [DOI: 10.1039/c7an01154g] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Herein, we review and summarise the development and biological applications of DNA tetrahedron, including cellular biosensors and drug delivery systems.
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Affiliation(s)
- Nuli Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Shiyuan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Institute of Biology
- Hunan University
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
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Xu F, Dong H, Cao Y, Lu H, Meng X, Dai W, Zhang X, Al-Ghanim KA, Mahboob S. Ultrasensitive and Multiple Disease-Related MicroRNA Detection Based on Tetrahedral DNA Nanostructures and Duplex-Specific Nuclease-Assisted Signal Amplification. ACS APPLIED MATERIALS & INTERFACES 2016; 8:33499-33505. [PMID: 27960393 DOI: 10.1021/acsami.6b12214] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A highly sensitive and multiple microRNA (miRNA) detection method by combining three-dimensional (3D) DNA tetrahedron-structured probes (TSPs) to increase the probe reactivity and accessibility with duplex-specific nuclease (DSN) for signal amplification for sensitive miRNA detection was proposed. Briefly, 3D DNA TSPs labeled with different fluorescent dyes for specific target miRNA recognition were modified on a gold nanoparticle (GNP) surface to increase the reactivity and accessibility. Upon hybridization with a specific target, the TSPs immobilized on the GNP surface hybridized with the corresponding target miRNA to form DNA-RNA heteroduplexes, and the DSN can recognize the formed DNA-RNA heteroduplexes to hydrolyze the DNA in the heteroduplexes to produce a specific fluorescent signal corresponding to a specific miRNA, while the released target miRNA strands can initiate another cycle, resulting in a significant signal amplification for sensitive miRNA detection. Different targets can produce different fluorescent signals, leading to the development of a sensitive detection for multiple miRNAs in a homogeneous solution. Under optimized conditions, the proposed assay can simultaneously detect three different miRNAs in a homogeneous solution with a logarithmic linear range spanning 5 magnitudes (10-12-10-16) and achieving a limit of detection down to attomolar concentrations. Meanwhile, the proposed miRNA assay exhibited the capability of discriminating single bases (three bases mismatched miRNAs) and showed good eligibility in the analysis of miRNAs extracted from cell lysates and miRNAs in cell incubation media, which indicates its potential use in biomedical research and clinical analysis.
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Affiliation(s)
- Fang Xu
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Haifeng Dong
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Yu Cao
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Huiting Lu
- School of Space and Environment, Beihang University , Beijing 100191, P. R. China
| | - Xiangdan Meng
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Wenhao Dai
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Bioengineering, University of Science & Technology Beijing , Beijing 100083, P. R. China
| | - Khalid Abdullah Al-Ghanim
- Department of Zoology, College of Science, P.O. Box 2455, King Saud University , Riyadh 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, Government College University , Faisalabad, Pakistan
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Affiliation(s)
- Yan Du
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, Jilin China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, Jilin China
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Meng F, Miao P, Wang B, Tang Y, Yin J. Identification of glutathione by voltammetric analysis with rolling circle amplification. Anal Chim Acta 2016; 943:58-63. [DOI: 10.1016/j.aca.2016.09.035] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/29/2016] [Accepted: 09/20/2016] [Indexed: 01/17/2023]
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50
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Cheng W, Yan W, Miao P. TNF-α responsive DNA star trigon formation from four hairpin probes and the analytical application. Sci China Chem 2016. [DOI: 10.1007/s11426-016-0259-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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