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Huang T, Lu Z, Mo P, Liu P, Liu S, Peng J, Li R, Jia N, Li M, Dai Z, Chen J, Chen J. A DNA walker based on hairpin-shaped DNA aligner and fueled by nicking endonuclease for sensitive and rapid miRNA analysis. Anal Chim Acta 2024; 1316:342873. [PMID: 38969432 DOI: 10.1016/j.aca.2024.342873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND DNA walker-based strategies have gained significant attention in nucleic acid analysis. However, they face challenges related to balancing design complexity, sequence dependence, and amplification efficiency. Furthermore, most existing DNA walkers rely on walking and lock probes, requiring optimization of various parameters like DNA probe sequence, walking-to-lock probe ratio, lock probe length, etc. to achieve optimal performance. This optimization process is time-consuming and adds complexity to experiments. To enhance the performance and reliability of DNA walker nanomachines, there is a need for a simpler, highly sensitive, and selective alternative strategy. RESULTS A sensitive and rapid miRNA analysis strategy named hairpin-shaped DNA aligner and nicking endonuclease-fueled DNA walker (HDA-NE DNA walker) was developed. The HDA-NE DNA walker was constructed by modifying hairpin-shaped DNA aligner (HDA) probe and substrate report (SR) probe on the surface of AuNPs. Under normal conditions, HDA and SR remained stable. However, in the presence of miR-373, HDA underwent a conformational transition to an activated structure to continuously cleave the SR probe on the AuNPs with the assistance of Nt.AlwI nicking endonuclease, resulting in sensitive miRNA detection with a detection limit as low as 0.23 pM. Additionally, the proposed HDA-NE DNA walker exhibited high selectivity in distinguishing miRNAs with single base differences and can effectively analyze miR-373 levels in both normal and breast cancer patient serums. SIGNIFICANCE The proposed HDA-NE DNA walker system was activated by a conformational change of HDA probe only in the presence of the target miRNA, eliminating the need for a lock probe and without sequence dependence for SR probe. This strategy demonstrated a rapid reaction rate of only 30 min, minimal background noise, and a high signal-to-noise ratio (S/B) compared to capture/lock-based DNA walker. The method is expected to become a powerful tool and play an important role in disease diagnosis and precision therapy.
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Affiliation(s)
- Ting Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhenbang Lu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Peixian Mo
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Piao Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Simin Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jing Peng
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Rongtian Li
- Southern University of Science and Technology Hospital, Shenzhen, 518055, China
| | - Nuan Jia
- Southern University of Science and Technology Hospital, Shenzhen, 518055, China.
| | - Minmin Li
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, 510632, China.
| | - Zong Dai
- School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Jinxiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, Guangdong-Hong Kong-Macao Joint Laboratory for New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
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Wang H, Shen M, Shen X, Liu J, Huang W, Jiang X, Liu H, Zeng S, Nan K, Cai S. An enzyme-free sensing platform for miRNA detection and in situ imaging in clinical samples based on DNAzyme cleavage-triggered catalytic hairpin assembly. Biosens Bioelectron 2024; 256:116279. [PMID: 38608496 DOI: 10.1016/j.bios.2024.116279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
MicroRNA (miRNA) is demonstrated to be associated with the occurrence and development of various diseases including cancer. Currently, most miRNA detection methods are confined to in vitro detection and cannot obtain information on the temporal and spatial expression of miRNA in relevant tissues and cells. In this work, we established a novel enzyme-free method that can be applied to both in vitro detection and in situ imaging of miRNA by integrating DNAzyme and catalytic hairpin assembly (CHA) circuits. This developed CHA-Amplified DNAzyme miRNA (CHAzymi) detection system can realize the quantitively in vitro detection of miR-146b (the biomarker of papillary thyroid carcinoma, PTC) ranging from 25 fmol to 625 fmol. This strategy has also been successfully applied to in situ imaging of miR-146b both in human PTC cell TPC-1 and clinical samples, showing its capacity as an alternative diagnostic method for PTC. Furthermore, this CHAzymi system can be employed as a versatile sensing platform for various miRNAs by revising the relevant sequences. The results imply that this system may expand the modality of miRNA detection and show promise as a novel diagnostic tool in clinical settings, providing valuable insights for effective treatment and management of the disease.
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Affiliation(s)
- Hechen Wang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minzhe Shen
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xudan Shen
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiatong Liu
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wenwen Huang
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xianfeng Jiang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China
| | - Hui Liu
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310020, China
| | - Su Zeng
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kewang Nan
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Department of Gastroenterology Surgery of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Jinhua Institute of Zhejiang University, Jinhua, 321299, China.
| | - Sheng Cai
- State Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Jinhua Institute of Zhejiang University, Jinhua, 321299, China.
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3
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Bi S, Chen W, Fang Y, Shen J, Zhang Q, Guo H, Ju H, Liu Y. Cancer Cell-Selective PD-L1 Inhibition via a DNA Safety Catch to Enhance Immunotherapy Specificity. Angew Chem Int Ed Engl 2024; 63:e202402522. [PMID: 38421189 DOI: 10.1002/anie.202402522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/02/2024]
Abstract
Immune checkpoint protein blockade (ICB) has emerged as a powerful immunotherapy approach, but suppressing immune-related adverse events (irAEs) for noncancerous cells and normal tissues remains challenging. Activatable ICB has been developed with tumor microenvironment highly-expressed molecules as stimuli, but they still lack precision and efficiency considering the diffusion of stimuli molecules in whole tumor tissue. Here we assemble PD-L1 with a duplex DNA strand, termed as "safety catch", to regulate its accessibility for ICB. The safety catch remains at "on" status for noncancerous cells to prevent ICB binding to PD-L1. Cancer cell membrane protein c-Met acts as a trigger protein to react with safety catch, which selectively exposes its hybridization region for ICB reagent. The ICB reagent is a retractable DNA nanostring with repeating hairpin-structural units, whose contraction drives PD-L1 clustering with endocytosis-guided degradation. The safety catch, even remained at "safety on" status, is removed from the cell membrane via a DNA strand displacement reaction to minimize its influence on noncancerous cells. This strategy demonstrates selective and potent immunotherapeutic capabilities only against cancer cells both in vitro and in vivo, and shows effective suppression of irAEs in normal tissues, therefore would become a promising approach for precise immunotherapy in mice.
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Affiliation(s)
- Shiyi Bi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Wei Chen
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jieyu Shen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Qing Zhang
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Hongqian Guo
- Department of Urology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, 210008, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
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4
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Wei Z, Yang X, Xu L, Benma L, Wu D, Zeng H. Microsphere-Enhanced Fluorescence-Lightened Solid-Phase Hybridization Assay: The Strategy to Highly Selective Detection of Micro Ribonucleic Acids. Anal Chem 2024; 96:6738-6745. [PMID: 38642036 DOI: 10.1021/acs.analchem.4c00365] [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: 04/22/2024]
Abstract
The detection of low-abundance microribonucleic acid (miRNA) frequently adopted nucleic acid sequence-based amplification detection, which was found to have poor selectivity for the nonspecific amplification of template-dependent ligation in enzyme-mediated cascade reactions. Here, a highly selective detection of miRNAs was developed that combined microsphere-enhanced fluorescence (MSEF) and solid-phase base-paired hybridization. The target miRNA could be accurately and quantitatively identified through the solid-phase hybridization assay on the surface of an optical microsphere, while the detected fluorescence signal could be physically amplified by MSEF. Hereinto, the optical microsphere acted as the fluorescence amplifier and whose surface supplied the space to carry out base-paired hybridization to recognize the target miRNA via the immobilized capture DNA sequence. The detected fluorescence signal of the single-base mismatched miRNA-21 sequence was just around 12% of that of the target miRNA-21 sequence in the measurement of model miRNA-21, while the limit of detection of miRNA-21 could be 1.0 fM. The developed detection of miRNA on an optical microsphere was demonstrated to be an excellent physically amplified method to selectively and sensitively detect the target miRNA and magnificently avoid the nonspecific amplification and false-positive results, which is expected to have wide applications in pathematology, pharmacology, clinic diagnosis, and on-site screening fields as well.
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Affiliation(s)
- Ziheng Wei
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Xiaoli Yang
- Department of Neurology, Shanghai fifth People's Hospital, Fudan University, 801 Heqing Road, Minhang District, Shanghai 200240, China
| | - Lingrui Xu
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Lamu Benma
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Danhong Wu
- Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | - Hulie Zeng
- Department of Neurology, Shanghai fifth People's Hospital, Fudan University, 801 Heqing Road, Minhang District, Shanghai 200240, China
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5
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Zhan Y, Mao Y, Sun P, Liu C, Gou H, Qi H, Chen G, Hu S, Tian B. Tumor-associated antigen-specific cell imaging based on upconversion luminescence and nucleic acid rolling circle amplification. Mikrochim Acta 2024; 191:248. [PMID: 38587676 DOI: 10.1007/s00604-024-06331-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/24/2024] [Indexed: 04/09/2024]
Abstract
Tumor-associated antigen (TAA)-based diagnosis has gained prominence for early tumor screening, treatment monitoring, prognostic assessment, and minimal residual disease detection. However, limitations such as low sensitivity and difficulty in extracting non-specific binding membrane proteins still exist in traditional detection methods. Upconversion luminescence (UCL) exhibits unique physical and chemical properties under wavelength near-infrared light excitation. Rolling circle amplification (RCA) is an efficient DNA amplification technique with amplification factors as high as 105. Therefore, the above two excellent techniques can be employed for highly accurate imaging analysis of tumor cells. Herein, we developed a novel nanoplatform for TAA-specific cell imaging based on UCL and RCA technology. An aptamer-primer complex selectively binds to Mucin 1 (MUC1), one of TAA on cell surface, to trigger RCA reaction, generating a large number of repetitive sequences. These sequences provide lots of binding sites for complementary signal probes, producing UCL from lanthanide-doped upconversion nanoparticles (UCNPs) after releasing quencher group. The experimental results demonstrate the specific attachment of upconversion nanomaterials to cancer cells which express a high level of MUC1, indicating the potential of UCNPs and RCA in tumor imaging.
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Affiliation(s)
- Ying Zhan
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Pei Sun
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Chenbin Liu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R. China
| | - Hongquan Gou
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R. China
| | - Haipeng Qi
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R. China
- School of Medicine, Anhui University of Science and Technology, Huainan, 232000, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China.
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, P. R. China.
| | - Bo Tian
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China.
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6
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Zhang M, Zhang Y, Wang Q, Liu K, Li L, Yu Z, Hou L, Zhang X, Zhao H, Cheng W, Zhang W. An APE1 gated signal amplified biosensor driven by catalytic hairpin assembly for the specific imaging of microRNA in situ. Int J Biol Macromol 2024; 262:129902. [PMID: 38307426 DOI: 10.1016/j.ijbiomac.2024.129902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024]
Abstract
In situ imaging of microRNA (miRNA) content and distribution is valuable for monitoring tumor progression. However, tumor specific in situ imaging remains a challenge due to low miRNA abundance, lack of biological compatibility, and poor specificity. In this study, we designed a DNA tetrahedral framework complex with hairpins (DTF-HPAP) consisting of an apurinic/apyrimidinic site (AP site) that could be specifically recognized and cleaved by apurinic/apyrimidinic endonuclease 1 (APE1). Efficient and specific in situ imaging of miR-21 in tumors was thus achieved through catalytic hairpin assembly (CHA) reaction. In this study, DTF-HPAP was successfully constructed to trigger the cumulative amplification of fluorescence signal in situ. The specificity, sensitivity and serum stability of DTF-HPAP were verified in vitro, and DTF-HPAP could be easily taken up by cells, acting as a biosensor to detect tumors in mice. Furthermore, we verified the ability of DTF-HPAP to specifically image miR-21 in tumors, and demonstrated its capability for tumor-specific imaging in clinical samples.
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Affiliation(s)
- Mengxin Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Qionglin Wang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China; Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Kangbo Liu
- Henan Medical Equipment Inspection Institute, Zhengzhou 450018, China
| | - Lifeng Li
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Zhidan Yu
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Ligong Hou
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Xianwei Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Huan Zhao
- Department of oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450018, China
| | - Weyland Cheng
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China; Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China.
| | - Wancun Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China; Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China; Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China.
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7
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Guo H, Chen J, Feng Y, Dai Z. A Simple and Robust Exponential Amplification Reaction (EXPAR)-Based Hairpin Template (exp-Hairpin) for Highly Specific, Sensitive, and Universal MicroRNA Detection. Anal Chem 2024; 96:2643-2650. [PMID: 38295438 DOI: 10.1021/acs.analchem.3c05323] [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: 02/02/2024]
Abstract
Specific and sensitive detection of microRNAs continues to encounter significant challenges, especially in the development of rapid and efficient isothermal amplification strategies for point-of-care settings. The exponential amplification reaction (EXPAR) has garnered significant attention owing to its simplicity and rapid amplification of signals within a short period. However, a substantial loss of amplification efficiency, difficulty in distinguishing closely related homologous sequences, and adapting the designed templates to other targets seriously hamper the practical application of the EXPAR. In this work, a hairpin template tailored for the EXPAR system (exp-Hairpin) was constructed by adding identical trigger sequences and enzyme cleavage sites on two arms of the hairpin, achieving theoretically more than 2n amplification efficiency and minimal background amplification of EXPAR. Modulating the stability of the exp-Hairpin template by increasing the stem length, the specificity of detecting target miRNA in highly homologous sequences could be significantly improved. Using miRNA let-7a as a target model, the exp-Hairpin with 8 bp stem length for EXPAR amplification curves could effectively distinguish target let-7a and nontarget let-7b/7c/7f/7g/7i homologous sequences. This strategy enabled the sensitive and accurate analysis of let-7a in diluted human serum with satisfactory recoveries. By simply replacing the loop recognition sequence of exp-Hairpin, the specific detection of miR-200b was also achieved, demonstrating the universality of this strategy. The exp-Hairpin EXPAR accelerates simple and rapid molecular diagnostic applications for short nucleic acids.
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Affiliation(s)
- Haijing Guo
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Yaqiang Feng
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou 510006, PR China
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8
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Guo S, Xie H, Zhao X, He H, Feng X, Li Y, Liu BF, Chen P. All-in-one detection of breast cancer-derived exosomal miRNA on a pen-based paper chip. Analyst 2024; 149:1250-1261. [PMID: 38225883 DOI: 10.1039/d3an02032k] [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: 01/17/2024]
Abstract
Exosomal microRNAs (miRNAs) play a pivotal role in intercellular communication, regulating gene expression in target cells, and hold significant promise as cancer biomarkers for early detection and screening. However, achieving precise and viable detection of exosomal miRNAs remains a challenge. This paper proposes an all-in-one detection strategy for breast cancer-derived exosomal miRNA-21 on a pen-based paper chip (PPC). The PPC is constructed using a modified automatic pen and lateral flow assay (LFA), which results in a cost-effective fabrication process. The user only needs to add the sample and trigger the top of the self-contained PPC after a period of time to complete the entire detection process. To enhance the sensitivity of exosomal miRNA testing, an enzyme-free catalyzed hairpin assembly (CHA) is further introduced, enabling highly sensitive detection of miRNA-21 with a limit of detection (LOD) of 25 fmol. Additionally, the detection of miRNAs in differentially-expressed cells and clinical samples has also been successfully achieved with high specificity. Overall, the proposed PPC provides an effective tool for detecting early cancer, monitoring diseases, and establishing point of care testing (POCT).
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Affiliation(s)
- Song Guo
- Department of Anesthesiology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, China
| | - Han Xie
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Xudong Zhao
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | | | - Xiaojun Feng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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9
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Fan C, Xie L, Zhao F, Wang J, Lin X, Chen X. Novel fluorescence nano-orbital biosensor for highly sensitive microRNA detection. Anal Chim Acta 2024; 1288:342172. [PMID: 38220303 DOI: 10.1016/j.aca.2023.342172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/18/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND MicroRNAs play an important role in regulating cell function and gene expression. Early prevention and clinical diagnosis of diseases have high requirements for high-sensitivity detection of microRNAs. Due to the limitations of tedious operation and large sample size, miRNA with small molecular weight and low expression abundance cannot be accurately detected in traditional miRNA detection. To improve the sensitivity and accuracy of detection, we established a novel biosensor based on nucleic acid circuit of signal amplification, which converted miRNA recognition into a fluorescence signal for amplification. RESULTS We designed a biosensor based on an exponential amplification reaction with cascaded HCR and DNAzyme nucleic acid circuit (named E-NOF biosensor) by amplicon sub-fragments to trigger the construction of fluorescence nano-orbitals (NOF), which could be used to detect miRNA ultrasensitively. By modifying two fluorophores (Cy3 and Cy5) on the chain of constructing nano-orbitals, when the amplicon triggered the construction of nano-orbitals, fluorescence resonance energy transfer (FRET) occurred between Cy3 and Cy5, and then two fluorescence signals with different trends could be observed. Therefore, through the ratio of the two signals, we could quantitatively and quickly detect the miRNA from 1 fM to 100 nM, and the E-NOF biosensor detection limit was as low as 0.129 fM. Furthermore, the HCR nucleic acid circuit cascaded with DNAzyme could enrich the fluorophores on the nano-orbitals and significantly enhance the fluorescence signal by accelerating the reaction rate. SIGNIFICANCE According to our understanding, the E-NOF biosensor is the first strategy to cascade EXPAR with HCR and DNAzyme nucleic acid circuit for miRNA-1246 detection. Accurate results can be obtained in only 120 min. Compared with the traditional HCR system, the sensitivity of the new E-NOF biosensor is increased by 1 × 109 times. Furthermore, the biosensor can also detect biomarkers in human serum samples. It has great potential in miRNA detection and identification.
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Affiliation(s)
- Cong Fan
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China
| | - Longjie Xie
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China
| | - Feng Zhao
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China; Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Jingjing Wang
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China
| | - Xiandong Lin
- Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Xian Chen
- College of Chemistry, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350116, China.
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10
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Pan W, Niu H, Luo S, Chen L, Wu ZS. Intelligent Reconfiguration-Promoted Cellular Internalization of Core-Shell DNA Nanoprobe Equipped with Successive Dual Stimuli-Responsive Protective Satellites for Amplification Fluorescence Imaging of Tumor Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2311388. [PMID: 38282377 DOI: 10.1002/smll.202311388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Indexed: 01/30/2024]
Abstract
Although DNA probes have attracted increasing interest for precise tumor cell identification by imaging intracellular biomarkers, the requirement of commercial transfection reagents, limited targeting ligands, and/or non-biocompatible inorganic nanostructures has hampered the clinic translation. To circumvent these shortcomings, a reconfigurable ES-NC (Na+ -dependent DNAzyme (E)-based substrate (S) cleavage core/shell DNA nanocluster (NC)) entirely from DNA strands is assembled for precise imaging of cancerous cells in a successive dual-stimuli-responsive manner. This nanoprobe is composed of a strung DNA tetrahedral satellites-based protective (DTP) shell, parallelly aligned target-responsive sensing (PTS) interlayer, and hydrophobic cholesterol-packed innermost layer (HCI core). Tetrahedral axial rotation-activated reconfiguration of DTP shell promotes the exposure of interior hydrophobic moieties, enabling cholesterol-mediated cellular internalization without auxiliary elements. Within cells, over-expressed glutathione triggers the disassembly of the DTP protective shell (first stimulus), facilitating target-stimulated signal transduction/amplification process (second stimuli). Target miRNA-21 is detected down to 10.6 fM without interference from coexisting miRNAs. Compared with transfection reagent-mediated counterpart, ES-NC displays a higher imaging ability, resists nuclease degradation, and has no detectable damage to healthy cells. The blind test demonstrates that the ES-NC is suitable for the identification of cancerous cells from healthy cells, indicating a promising tool for early diagnosis and prediction of cancer.
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Affiliation(s)
- Wenhao Pan
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Huimin Niu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
- Fujian Key Laboratory of Aptamers Technology, The 900th Hospital of Joint Logistics Support Force, Fuzhou, 350025, China
| | - Shasha Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Linhuan Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zai-Sheng Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
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11
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Xu H, Wu X, Liu Q, Yang C, Shen M, Wang Y, Liu S, Zhao S, Xiao T, Sun M, Ding Z, Bao J, Chen M, Gao M. A Universal Strategy for Enhancing the Circulating miRNAs' Detection Performance of Rolling Circle Amplification by Using a Dual-Terminal Stem-Loop Padlock. ACS NANO 2024; 18:436-450. [PMID: 38149638 PMCID: PMC10786163 DOI: 10.1021/acsnano.3c07721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023]
Abstract
Rolling circle amplification (RCA) is one of the most promising nucleic acid detection technologies and has been widely used in the molecular diagnosis of disease. Padlock probes are often used to form circular templates, which are the core of RCA. However, RCA often suffers from insufficient specificity and sensitivity. Here we report a reconstruction strategy for conventional padlock probes to promote their overall performance in nucleic acid detection while maintaining probe functions uncompromised. When two rationally designed stem-loops were strategically placed at the two terminals of linear padlock probes, the specificity of target recognition was enhanced and the negative signal was significantly delayed. Our design achieved the best single-base discrimination compared with other structures and over a 1000-fold higher sensitivity than that of the conventional padlock probe, validating the effectiveness of this reconstruction. In addition, the underlying mechanisms of our design were elucidated through molecular dynamics simulations, and the versatility was validated with longer and shorter padlocks targeting the same target, as well as five additional targets (four miRNAs and dengue virus - 2 RNA mimic (DENV-2)). Finally, clinical applicability in multiplex detection was demonstrated by testing real plasma samples. Our exploration of the structures of nucleic acids provided another perspective for developing high-performance detection systems, improving the efficacy of practical detection strategies, and advancing clinical diagnostic research.
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Affiliation(s)
- Hanqing Xu
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Xianlan Wu
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Qian Liu
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Cheng Yang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Man Shen
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Yingran Wang
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Shuai Liu
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Shuang Zhao
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Ting Xiao
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Minghui Sun
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Zishan Ding
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Jing Bao
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
| | - Ming Chen
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
- College
of Pharmacy and Laboratory Medicine, Third
Military Medical University (Army Medical University), 30 Gaotanyan, Shapingba District, Chongqing 400038, P. R. China
| | - Mingxuan Gao
- Department
of Clinical Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, P. R. China
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12
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Ren X, Wu Y, Deng R, Li J. Single-Cell Imaging of mRNA by Target RNA-Initiated RCA. Methods Mol Biol 2024; 2822:65-75. [PMID: 38907912 DOI: 10.1007/978-1-0716-3918-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
We present a powerful method for direct mRNA detection based on ligation-based recognition and in situ amplification, capable of single-cell imaging mRNA at single-nucleotide and single-molecule resolution. Attributed to the use of Splint R ligase that can ligate padlock probe with RNA as target template, this method can efficiently detect mRNA in the absence of reverse transcription. This method enables spatial localization and correlation analysis of gene expression in single cells, which helps us to elucidate gene function and regulatory mechanisms.
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Affiliation(s)
- Xiaojun Ren
- Department of Chemistry, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Yifan Wu
- Department of Chemistry, College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, China
| | - Jinghong Li
- Beijing Life Science Academy, Beijing, China.
- Department of Chemistry, Center for BioAnalytical Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China.
- New Cornerstone Science Laboratory, Shenzhen, China.
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, China.
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13
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Yan H, Wen Y, Tian Z, Hart N, Han S, Hughes SJ, Zeng Y. A one-pot isothermal Cas12-based assay for the sensitive detection of microRNAs. Nat Biomed Eng 2023; 7:1583-1601. [PMID: 37106152 PMCID: PMC11108682 DOI: 10.1038/s41551-023-01033-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 03/29/2023] [Indexed: 04/29/2023]
Abstract
The use of microRNAs as clinical cancer biomarkers is hindered by the absence of accurate, fast and inexpensive assays for their detection in biofluids. Here we report a one-step and one-pot isothermal assay that leverages rolling-circle amplification and the endonuclease Cas12a for the accurate detection of specific miRNAs. The assay exploits the cis-cleavage activity of Cas12a to enable exponential rolling-circle amplification of target sequences and its trans-cleavage activity for their detection and for signal amplification. In plasma from patients with pancreatic ductal adenocarcinoma, the assay detected the miRNAs miR-21, miR-196a, miR-451a and miR-1246 in extracellular vesicles at single-digit femtomolar concentrations with single-nucleotide specificity. The assay is rapid (sample-to-answer times ranged from 20 min to 3 h), does not require specialized instrumentation and is compatible with a smartphone-based fluorescence detection and with the lateral-flow format for visual readouts. Simple assays for the detection of miRNAs in blood may aid the development of miRNAs as biomarkers for the diagnosis and prognosis of cancers.
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Affiliation(s)
- He Yan
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Yunjie Wen
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zimu Tian
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Nathan Hart
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Song Han
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA
| | - Steven J Hughes
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, USA
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, USA.
- University of Florida Health Cancer Center, Gainesville, FL, USA.
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14
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Liu WJ, Wang LJ, Zhang CY. Progress in quantum dot-based biosensors for microRNA assay: A review. Anal Chim Acta 2023; 1278:341615. [PMID: 37709484 DOI: 10.1016/j.aca.2023.341615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/15/2023] [Accepted: 07/11/2023] [Indexed: 09/16/2023]
Abstract
MicroRNAs (miRNAs) are responsible for post-transcriptional gene regulation, and may function as valuable biomarkers for diseases diagnosis. Accurate and sensitive analysis of miRNAs is in great demand. Quantum dots (QDs) are semiconductor nanomaterials with superior optoelectronic features, such as high quantum yield and brightness, broad absorption and narrow emission, long fluorescence lifetime, and good photostability. Herein, we give a comprehensive review about QD-based biosensors for miRNA assay. Different QD-based biosensors for miRNA assay are classified by the signal types including fluorescent, electrochemical, electrochemiluminescent, and photoelectrochemical outputs. We highlight the features, principles, and performances of the emerging miRNA biosensors, and emphasize the challenges and perspectives in this field.
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Affiliation(s)
- Wen-Jing Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Li-Juan Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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15
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Su J, Wang M, Lin P, Huang Z, Li G, Chen X, Yan H, Zhou L. Trigger-activated autonomous DNA machine for amplified liver cancer biomarker microRNA21 imaging. ANAL SCI 2023; 39:1661-1667. [PMID: 37552462 DOI: 10.1007/s44211-023-00397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/03/2022] [Indexed: 08/09/2023]
Abstract
MicroRNA-21 (miRNA-21) is a kind of RNA that exists in biological fluids such as blood, urine and saliva. It has over expression in liver cancer and has different expression in different stages of cancer. However, due to the characteristics of small base number, short length, low abundance and easy degradation of miRNA-21, the detection of miRNA-21 is a challenging subject. Visualization, sensitive, specific and stable detection of tumor suppressor or oncogene microRNAs (miRNAs) remains challenging and is highly significant for clinical diagnostics. To solve this problem, we have developed a target-triggered hybridization assembly DNA machine for intracellular miRNA imaging based on strand displacement amplification (SDA) and branched hybridization chain reaction (B-HCR). In this approach, the target miRNA could hybridize with the template probe to trigger the SDA, resulting in the formation of nicked fragments (NFs) that hybridized with hairpin probe1 (HP1). The opened HP1 could hybridize with hairpin probe2 (HP2), leading to the self-assembly of hyperbranched DNA nanostructures through B-HCR. As expected, the newly developed method exhibits a detection limit down to 11.3 pM miRNA-21 and achieves high selectivity toward miRNA-21 against other interfering miRNAs. Due to its superior sensitivity and selectivity, our method can be further used to detect miRNA-21 in human serum samples. By taking advantage of intelligent design, the proposed method was also used for image miRNA-21 expression levels in different cell lines. This method shows a broad application in clinical diagnosis.
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Affiliation(s)
- Jiqin Su
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Maolin Wang
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Peiyi Lin
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Zhishu Huang
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Guibin Li
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Xiangru Chen
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China
| | - Huidi Yan
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China.
| | - Lixin Zhou
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, Fujian, China.
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16
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Su J, Sun C, Du J, Xing X, Wang F, Dong H. RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy. Adv Healthc Mater 2023; 12:e2300367. [PMID: 37084038 DOI: 10.1002/adhm.202300367] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Indexed: 04/22/2023]
Abstract
Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.
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Affiliation(s)
- Jiaxin Su
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Chenyang Sun
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Jinya Du
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
| | - Xiaotong Xing
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
| | - Fang Wang
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen, Guangdong, 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry & Biological Engineering, University of Science & Technology Beijing, 30 Xueyuan Road, Beijing, 100083, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong, 518060, China
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17
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Wu K, Ma C, Wang Y. Functional Nucleic Acid Probes Based on Two-Photon for Biosensing. BIOSENSORS 2023; 13:836. [PMID: 37754070 PMCID: PMC10527542 DOI: 10.3390/bios13090836] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023]
Abstract
Functional nucleic acid (FNA) probes have been widely used in environmental monitoring, food analysis, clinical diagnosis, and biological imaging because of their easy synthesis, functional modification, flexible design, and stable properties. However, most FNA probes are designed based on one-photon (OP) in the ultraviolet or visible regions, and the effectiveness of these OP-based FNA probes may be hindered by certain factors, such as their potential for photodamage and limited light tissue penetration. Two-photon (TP) is characterized by the nonlinear absorption of two relatively low-energy photons of near-infrared (NIR) light with the resulting emission of high-energy ultraviolet or visible light. TP-based FNA probes have excellent properties, including lower tissue self-absorption and autofluorescence, reduced photodamage and photobleaching, and higher spatial resolution, making them more advantageous than the conventional OP-based FNA probes in biomedical sensing. In this review, we summarize the recent advances of TP-excited and -activated FNA probes and detail their applications in biomolecular detection. In addition, we also share our views on the highlights and limitations of TP-based FNA probes. The ultimate goal is to provide design approaches for the development of high-performance TP-based FNA probes, thereby promoting their biological applications.
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Affiliation(s)
- Kefeng Wu
- GBA Branch of Aerospace Information Research Institute, Chinese Academy of Sciences, Guangzhou 510700, China
- Guangdong Provincial Key Laboratory of Terahertz Quantum Electromagnetics, Guangzhou 510700, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Yisen Wang
- GBA Branch of Aerospace Information Research Institute, Chinese Academy of Sciences, Guangzhou 510700, China
- Guangdong Provincial Key Laboratory of Terahertz Quantum Electromagnetics, Guangzhou 510700, China
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18
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Slott S, Krüger-Jensen CS, Ferreira da Silva I, Pedersen NB, Astakhova K. Mutations in microRNA-128-2-3p identified with amplification-free hybridization assay. PLoS One 2023; 18:e0289556. [PMID: 37607185 PMCID: PMC10443835 DOI: 10.1371/journal.pone.0289556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/20/2023] [Indexed: 08/24/2023] Open
Abstract
We describe a quantitative detection method for mutated microRNA in human plasma samples. Specific oligonucleotides designed from a Peyrard-Bishop model allowed accurate prediction of target:probe recognition affinity and specificity. Our amplification-free tandem bead-based hybridization assay had limit of detection of 2.2 pM. Thereby, the assay allowed identification of single-nucleotide polymorphism mismatch profiles in clinically relevant microRNA-128-2-3p, showing terminal mutations that correlate positively with inflammatory colitis and colorectal cancer.
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Affiliation(s)
- Sofie Slott
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | | | - Izabela Ferreira da Silva
- Programa Interunidades de Pós-Graduacão em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte-MG, Brazil
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte-MG, Brazil
- Bioinformatics Core, Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, House of Biomedicine II, Belvaux, Luxembourg
| | - Nadia Bom Pedersen
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
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19
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Watanabe H, Maehara D, Nishihara T, Tanabe K. Alkyne-tethered oligodeoxynucleotides that allow simultaneous detection of multiple DNA/RNA targets using Raman spectroscopy. RSC Adv 2023; 13:20756-20760. [PMID: 37441041 PMCID: PMC10334030 DOI: 10.1039/d3ra03861k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Detection of multiple DNA/RNA targets is essential for understanding cellular function. Herein, we propose a general method for the simultaneous detection of plural nucleic acids based on surface-enhanced Raman scattering (SERS) using gold nanoparticles bearing functional oligodeoxynucleotides (ODNs) on their surface. Modified ODNs bearing an acetylene tag hybridized with their complementary ODNs on the surface of the gold nanoparticles, inducing a strong SERS signal of the acetylene tag. The addition of the target nucleic acid to the system resulted in a spontaneous displacement of the strand on the particle and dissociation of the alkyne-tagged ODN from the particle, resulting in a dramatic decrease in signal intensity. By using an alkyne tag for each of the multiple target nucleic acids, each target could be detected simultaneously. In addition, we successfully detected cellular microRNA. Different targets showed changes with different wavenumbers in the Raman spectra, allowing for the detection of multiple nucleic acids.
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Affiliation(s)
- Hikaru Watanabe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara 252-5258 Japan
| | - Daigo Maehara
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara 252-5258 Japan
| | - Tatsuya Nishihara
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara 252-5258 Japan
| | - Kazuhito Tanabe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara 252-5258 Japan
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20
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Quazi MZ, Hwang J, Song Y, Park N. Hydrogel-Based Biosensors for Effective Therapeutics. Gels 2023; 9:545. [PMID: 37504424 PMCID: PMC10378974 DOI: 10.3390/gels9070545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Nanotechnology and polymer engineering are navigating toward new developments to control and overcome complex problems. In the last few decades, polymer engineering has received researchers' attention and similarly, polymeric network-engineered structures have been vastly studied. Prior to therapeutic application, early and rapid detection analyses are critical. Therefore, developing hydrogel-based sensors to manage the acute expression of diseases and malignancies to devise therapeutic approaches demands advanced nanoengineering. However, nano-therapeutics have emerged as an alternative approach to tackling strenuous diseases. Similarly, sensing applications for multiple kinds of analytes in water-based environments and other media are gaining wide interest. It has also been observed that these functional roles can be used as alternative approaches to the detection of a wide range of biomolecules and pathogenic proteins. Moreover, hydrogels have emerged as a three-dimensional (3D) polymeric network that consists of hydrophilic natural or synthetic polymers with multidimensional dynamics. The resemblance of hydrogels to tissue structure makes them more unique to study inquisitively. Preceding studies have shown a vast spectrum of synthetic and natural polymer applications in the field of biotechnology and molecular diagnostics. This review explores recent studies on synthetic and natural polymers engineered hydrogel-based biosensors and their applications in multipurpose diagnostics and therapeutics. We review the latest studies on hydrogel-engineered biosensors, exclusively DNA-based and DNA hydrogel-fabricated biosensors.
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Affiliation(s)
- Mohzibudin Z Quazi
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Jimin Hwang
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Youngseo Song
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
| | - Nokyoung Park
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Gyeonggi-do, Republic of Korea
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21
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Chen W, Liu F, Zhang C, Duan Y, Ma J, Wang Y, Chen G. A review of advances in aptamer-based cell detection technology. Mol Biol Rep 2023; 50:5425-5438. [PMID: 37101007 DOI: 10.1007/s11033-023-08410-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/24/2023] [Indexed: 04/28/2023]
Abstract
Since cells are the basic structural and functional units of organisms, the detection or quantitation of cells is one of the most common basic problems in life science research. The established cell detection techniques mainly include fluorescent dye labeling, colorimetric assay, and lateral flow assay, all of which employ antibodies as cell recognition elements. However, the widespread application of the established methods generally dependent on antibodies is limited, because the preparation of antibodies is complicated and time-consuming, and unrecoverable denaturation is prone to occur with antibodies. By contrast, aptamers that are generally selected through the systematic evolution of ligands by exponential enrichment can avoid the disadvantages of antibodies due to their controllable synthesis, thermostability, and long shelf life, etc. Accordingly, aptamers may serve as novel molecular recognition elements like antibodies in combination with various techniques for cell detection. This paper reviews the developed aptamer-based cell detection methods, mainly including aptamer-fluorescent labeling, aptamer-isothermal amplification assay, electrochemical aptamer sensor, aptamer-based lateral flow analysis, and aptamer-colorimetric assay. The principles, advantages, progress of application in cell detection and future development trend of these methods were specially discussed. Overall, different assays are suitable for different detection purposes, and the development of more accurate, economical, efficient, and rapid aptamer-based cell detection methods is always on the road in the future. This review is expected to provide a reference for achieving efficient and accurate detection of cells as well as improving the usefulness of aptamers in the field of analytical applications.
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Affiliation(s)
- Wenrong Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China.
| | - Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Jinju Ma
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, PR China
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, PR China.
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22
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Wang Y, Xiong Y, Duan Y, Shi K, Su C, Ding L, Wang J, He L. Activatable Fluorescence-Encoded Nanoprobes Enable Simple Multiplexed RNA Imaging in Live Cells. ACS Sens 2023; 8:1918-1928. [PMID: 37130214 DOI: 10.1021/acssensors.2c02657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Benefiting from superior programmable performance and flexible design of DNA technologies, a variety of single-molecule RNA fluorescence imaging methodologies have been reported. However, the multiplexing capability is restricted owing to the spectral overlap of fluorophores. To overcome this limitation, some inspiring multiplex imaging strategies have been developed, but in practice, it remains challenging to achieve convenient and rapid imaging in live cells due to complex designs and additional pretreatments to increase cell permeability. Here, we report an activatable fluorescence-encoded nanoprobe (AFENP) strategy, through which fluorescence-encoded functional modules for qualitative analysis and activated nucleic acid assemblies functional modules for quantitative testing enable simple multiplexed RNA imaging in single live cells. As a proof of principle, by two distinguishable fluorophores (fluorescein and rhodamine B) and their seven distinctly differentiated intensity levels, self-assembled AFENP enables simplified and quick simultaneous in situ detection and imaging of seven types of targets in live single cells because the fluorescent quantitative signal is activated only in the presence of target avoiding the washing procedures and additional pretreatment to increase cell permeability is undesired. We expect that this practical single-cell analysis platform will be adopted for multiple gene expression analysis and imaging in live cells on account of its simplicity and multiplex capability.
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Affiliation(s)
- Ya Wang
- College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Yamin Xiong
- School of Life Sciences, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Yanjuan Duan
- College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Kangqi Shi
- College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Chaojie Su
- College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Jia Wang
- College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Leiliang He
- College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
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23
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Ho V, Baker JR, Willison KR, Barnes PJ, Donnelly LE, Klug DR. Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells. Commun Biol 2023; 6:458. [PMID: 37100999 PMCID: PMC10133449 DOI: 10.1038/s42003-023-04845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3+ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.
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Affiliation(s)
- Vanessa Ho
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Jonathan R Baker
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Keith R Willison
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
| | - Peter J Barnes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Louise E Donnelly
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK.
| | - David R Klug
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
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24
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Zhang Y, Cai Q, Yan X, Jie G. Versatile fluorescence detection of T4 PNK and mRNA based on unique DNA nanomachine amplification. Anal Chim Acta 2023; 1251:341003. [PMID: 36925292 DOI: 10.1016/j.aca.2023.341003] [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: 01/09/2023] [Revised: 02/09/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
The development of DNA nanomachines provides a new strategy for the detection of tumor markers. In this work, an intelligent three-dimensional (3D) DNA walking machine with polynucleotide kinase (PNK) activator was designed, which was coupled with unique nanomachine formed by DNA nanowire cascade amplification reaction for versatile fluorescence detection of T4 PNK activity and messenger RNA (mRNA). When PNK exists, the free DNA walker was formed by hydrolysis cleavage of exonuclease, then the fluorophore-labeled report probe on the Au nanoparticles (NPs) was sheared during cycling cleavage reaction, thus the fluorescence signal was recovered for detection of PNK. Moreover, the DNA nanowires were produced by rolling ring amplification, then target mRNA sequentially initiated interval hybridization of hairpin probes through DNA nanowire, thus realizing DNA cascade reaction (DCR) with high "on" signal of DNA nanomachine for mRNA assay. This developed novel fluorescence nanomachine reported a new assay method with promising application for versatile targets and showed great potential for molecular-target therapies, and clinic diagnostics.
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Affiliation(s)
- Yuqi Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Qianqian Cai
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Xiaoshi Yan
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China
| | - Guifen Jie
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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25
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Wang X, Shepherd S, Li N, Che C, Song T, Xiong Y, Palm IR, Zhao B, Kohli M, Demirci U, Lu Y, Cunningham BT. A Target Recycling Amplification Process for the Digital Detection of Exosomal MicroRNAs through Photonic Resonator Absorption Microscopy. Angew Chem Int Ed Engl 2023; 62:e202217932. [PMID: 36622783 PMCID: PMC10073263 DOI: 10.1002/anie.202217932] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/10/2023]
Abstract
Exosomal microRNAs (miRNAs) have considerable potential as pivotal biomarkers to monitor cancer development, dis-ease progression, treatment effects and prognosis. Here, we report an efficient target recycling amplification process (TRAP) for the digital detection of miRNAs using photonic resonator absorption microscopy. We achieve multiplex digital detection with sub-attomolar sensitivity in 20 minutes, robust selectivity for single nucleotide variants, and a broad dynamic range from 1 aM to 1 pM. Compared with traditional qRT-PCR, TRAP showed similar accuracy in profiling exosomal miRNAs derived from cancer cells, but also exhibited at least 31-fold and 61-fold enhancement in the limits of miRNA-375 and miRNA-21 detection, respectively. The TRAP approach is ideal for exosomal or circulating miRNA biomarker quantification, where the miRNAs are present in low concentrations or sample volume, with potentials for frequent, low-cost, and minimally invasive point-of-care testing.
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Affiliation(s)
- Xiaojing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Skye Shepherd
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Nantao Li
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Congnyu Che
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Tingjie Song
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yanyu Xiong
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Isabella Rose Palm
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Bin Zhao
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Manish Kohli
- Department of Oncology, Mayo Clinic Rochester, MN 55905, USA; Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 12902, USA
| | - Utkan Demirci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology School of Medicine, Stanford University, Palo Alto, CA 94304, USA
| | - Yi Lu
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Brian T. Cunningham
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, Department of Electrical and Computer Engineering, Department of Chemistry, Department of Bioengineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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26
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Deng Y, Zhou T, Peng Y, Wang M, Xiang L, Zhang Y, Li J, Yang J, Li G. Dual-Gene-Controlled Rolling Circle Amplification Strategy for SARS-CoV-2 Analysis. Anal Chem 2023; 95:3358-3362. [PMID: 36723441 PMCID: PMC9897047 DOI: 10.1021/acs.analchem.2c04572] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/24/2023] [Indexed: 02/02/2023]
Abstract
The development of sensitive, accurate, and conveniently operated methods for the simultaneous assay of two nucleic acids is promising while still challenging. In this work, by using two genes (the N gene and RdRp gene) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as examples, we have designed an ingenious dual-gene-controlled rolling circle amplification (RCA) strategy to propose an accurate and sensitive electrochemical method. Specifically, the coexistence of the two target genes can trigger the RCA reaction to generate a number of repeated G-quadruplex (G4)-forming sequences. These sequences then switch into G4/hemin complexes with redox activity after the incubation of hemin, which can catalyze the TMB/H2O2 substrates to produce significantly enhanced current responses. Experimental results reveal that the proposed method exhibits satisfying feasibility and analytical performance, enabling the sensitive detection of SARS-CoV-2 in the range of 0.1-5000 pM, with the detection limit of 57 fM. Meanwhile, because only the simultaneous existence of the two target genes can effectively trigger the downstream amplification reaction, this method can effectively avoid false-positives and ensure specificity as well as accuracy. Furthermore, our method can distinguish the COVID-19 samples from healthy people, and the outcomes show a satisfying agreement with the results of RT-PCR, manifesting that our label-free dual-gene-controlled RCA strategy exhibits great possibility in clinical application.
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Affiliation(s)
- Ying Deng
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Tianci Zhou
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Ying Peng
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Minghui Wang
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Liangliang Xiang
- The Second Hospital of Nanjing, Nanjing
University of Chinese Medicine, Nanjing210003, P. R.
China
| | - Yuanyuan Zhang
- Department of Obstetrics and Gynecology,
The First Affiliated Hospital of Nanjing Medical University,
Nanjing210029, P. R. China
| | - Jinlong Li
- The Second Hospital of Nanjing, Nanjing
University of Chinese Medicine, Nanjing210003, P. R.
China
| | - Jie Yang
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
| | - Genxi Li
- State Key Laboratory of Analytical Chemistry for Life
Science, School of Life Sciences, Nanjing University,
Nanjing210023, P. R. China
- Center for Molecular Recognition and Biosensing,
School of Life Sciences, Shanghai University, Shanghai200444,
P. R. China
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27
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Paluzzi VE, Zhang C, Mao C. Near-Quantitative Preparation of Short Single-Stranded DNA Circles. Angew Chem Int Ed Engl 2023; 62:e202218443. [PMID: 36652628 DOI: 10.1002/anie.202218443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
Small, single-stranded DNA (ssDNA) circles have many applications, such as templating rolling circle amplification (RCA), capturing microRNAs, and scaffolding DNA nanostructures. However, it is challenging to prepare such ssDNA circles, particularly when the DNA size becomes very small (e.g. a 20 nucleotide (nt) long ssDNA circle). Often, such short ssDNA dominantly form concatemers (either linear or circular) due to intermolecular ligation, instead of forming monomeric ssDNA circles by intramolecular ligation. Herein, a simple method to overcome this problem by designing the complementary linker molecules is reported. It is demonstrated that ssDNA, as short as 16 nts, can be enzymatically ligated (by the commonly used T4 DNA ligase) into monomeric ssDNA circles at high concentration (100 μM) with high yield (97 %). This method does not require any special sequence, thus, it is expected to be generally applicable. The experimental protocol is identical to regular DNA ligation, thus, is expected to be user friendly for general chemists and biologists.
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Affiliation(s)
- Victoria E Paluzzi
- Purdue University, Department of Chemistry, West Lafayette, IN-47907, USA
| | - Cuizheng Zhang
- Purdue University, Department of Chemistry, West Lafayette, IN-47907, USA
| | - Chengde Mao
- Purdue University, Department of Chemistry, West Lafayette, IN-47907, USA
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28
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Xu H, Zheng Y, Chen D, Cheng Y, Fang X, Zhong C, Huang X, Huang Q, Xu J, Xu J, Xue C. Branch-Shaped Trapping Device Regulates Accelerated Catalyzed Hairpin Assembly and Its Application for MicroRNA In Situ Imaging. Anal Chem 2023; 95:1210-1218. [PMID: 36583970 DOI: 10.1021/acs.analchem.2c03956] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Enzyme-free DNA strand displacement process is often practical when detecting miRNAs expressed at low levels in living cells. However, the poor kinetics, tedious reaction period, and multicomponent system hamper its in vivo applications to a great extent. Herein, we design a branch-shaped trapping device (BTD)-based spatial confinement reactor and applied it for accelerated miRNA in situ imaging. The reactor consists of a pair of trapped probe-based catalyzed hairpin assembly (T-CHA) reactions attached around the BTD. The trapping device naturally offered CHA reactions a good spatial-confinement effect by integrating the metastable probes (MHPa and MHPb) of the traditional CHA with the four-branched arm of BTD, which greatly improved the localized concentration of probes and shortened their physical distance. The autonomous and progressive walk of miRNA on the four-arm nanoprobes via T-CHA can rapidly tie numerous four-arm nanoprobes into figure-of-eight nanoknots (FENs), yielding strong fluorescence that is proportional to the miRNA expression level. The unique nanoarchitecture of the FEN also benefits the restricted freedom of movement (FOM) in a confined cellular environment, which makes the system ideally suitable for in situ imaging of intracellular miRNAs. In vitro and in situ analyses also demonstrated that the T-CHA overall outperformed the dissociative probe-based CHA (D-CHA) in stability, reaction speed, and amplification sensitivity. The final application of the T-CHA-based four-arm nanoprobe for imagings of both cancer cells and normal cells shows the potential of the platform for accurately and timely revealing miRNA in biological systems.
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Affiliation(s)
- Huo Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Yanhui Zheng
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Danlong Chen
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Yinghao Cheng
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiaojun Fang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Chunlian Zhong
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Xinmei Huang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Qi Huang
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Jiawei Xu
- College of Materials and Chemical Engineering, Minjiang University, Fuzhou 350108, Fujian, China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chang Xue
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
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29
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Kim D, Lee J, Han J, Lim J, Lim EK, Kim E. A highly specific and flexible detection assay using collaborated actions of DNA-processing enzymes for identifying multiple gene expression signatures in breast cancer. Analyst 2023; 148:316-327. [PMID: 36484412 DOI: 10.1039/d2an01672a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most nucleic acid biosensors employ nucleic acid-processing enzymes to bind, degrade, splice, synthesize, and modify nucleic acids. Utilizing their unique substrate preference, binding mode, and catalytic activity is of great importance in designing nucleic acid biosensors. Combination with DNA-processing enzymes enables them to transform into a new generation of molecular diagnostics tools with enhanced selectivity and sensitivity and reduced reaction time. Here, we report an isothermal amplification strategy by coemploying a structure-specific endonuclease (flap endonuclease 1, FEN1) and a strand-displacing DNA polymerase (Bst DNA polymerase) to detect long RNA targets. This approach couples the FEN1-driven invasive cleavage reaction with toehold-mediated rolling circle amplification (iFEN-tRCA), enabling the highly selective and rapid detection of long RNA targets and offering a detection limit below 10 pM within 1 h. We used two targets, such as human epidermal growth factor receptor 2 (HER2, encoded by ERBB2) and dopamine- and cyclic AMP-regulated phosphoprotein (DARPP, encoded by PPP1R1B), associated with prognosis or response to anticancer therapy. We demonstrated the feasibility and quantitative capability of the iFEN-tRCA assay by assessing the expression of two RNA transcripts (ERBB2 and PPP1R1B) with total RNA extracts purified from human breast cancer cells. Therefore, we envision that the developed assay will provide a suitable prognostic and diagnostic tool for identifying appropriate patients for HER2-targeted therapy and predicting the clinical outcome and occurrence of metastasis relapse in breast cancer.
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Affiliation(s)
- Dain Kim
- Department of Bioengineering & Nano-bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon 22012, Republic of Korea.
| | - Jiyoung Lee
- Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
| | - Jueun Han
- Department of Chemistry, Incheon National University, Incheon 22012, Republic of Korea
| | - Jaewoo Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
| | - Eun-Kyung Lim
- BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea. .,Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, Daejeon 34113, Republic of Korea.,School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Eunjung Kim
- Department of Bioengineering & Nano-bioengineering, Research Center for Bio Materials and Process Development, Incheon National University, Incheon 22012, Republic of Korea. .,Division of Bioengineering, Incheon National University, Incheon 22012, Republic of Korea
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30
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Chen Y, Ye L, Chen H, Fan T, Qiu C, Chen Y, Jiang Y. Simple Isothermal and Label-Free Strategy for Colorectal Cancer Potential Biomarker miR-625-5p Detection. BIOSENSORS 2023; 13:78. [PMID: 36671913 PMCID: PMC9855811 DOI: 10.3390/bios13010078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/12/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
miRNA is considered a novel biomarker for cancer diagnosis and due to its low level in vivo, the development of new detection methods for it has become a research hotspot in recent years. Here, we firstly found that miR-625-5p was significantly upregulated in colorectal cancer tissues by means of differential expression analysis of the dbDEMC database and clinical validation. Subsequently, it was found that miR-625-5p promoted cell proliferation and migration but inhibited apoptosis through phenotypic experiments; thus, we initially identified miR-625-5p as a potential biomarker for colorectal cancer. Moreover, in order to monitor slight changes in the miR-625-5p level, we developed a novel detection method for it based on strand displacement amplification (SDA). In this system, a hairpin was designed to recognize and pair with miR-625-5p, which was used as a primer to initiate SDA, and a large number of complementary DNAs were generated via cyclic amplification, followed by the addition of SYBR Gold to achieve quantitative analysis of miR-625-5p. Moreover, this method showed a good response to miR-625-5p with a detection limit of 8.6 pM and a dynamic range of 0.01 to 200 nM, and the specificity of it was verified using a set of other miRNAs as an interference. Finally, we set up different concentrations of biologic samples for detection to verify the practicability of the method. The results of this study indicate that this detection method has great potential in clinical diagnosis.
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Affiliation(s)
- Yifei Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Lizhen Ye
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Tingting Fan
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
| | - Cheng Qiu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yuyang Jiang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
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31
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Qiu X, Liu C, Zhu C, Zhu L. MicroRNA Detection with CRISPR/Cas. Methods Mol Biol 2023; 2630:25-45. [PMID: 36689174 DOI: 10.1007/978-1-0716-2982-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Low-cost detection of miRNAs has caught broad attention in recent years due to the potential application of these small noncoding RNAs for diagnostics and therapeutic purposes. Their small size and low abundance, however, derive challenges in engineering robust detection tools. To date, multiple detection assays have been developed to achieve highly specific recognition of trace amount of miRNA with state-of-the-art nucleic acid detection and signal amplification techniques. In this chapter we describe how isothermal amplification techniques and CRISPR/Cas-based techniques can be integrated to generate rationally designed miRNA detection systems for specific miRNA.
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Affiliation(s)
- Xinyuan Qiu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, China
| | - Chuanyang Liu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, China
| | - Chushu Zhu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, China
- College of Intelligence Science and Technology, National University of Defense Technology, Changsha, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Science, National University of Defense Technology, Changsha, China.
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32
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Liu Q, Huang Y, Li Z, Li L, Zhao Y, Li M. An Enzymatically Gated Catalytic Hairpin Assembly Delivered by Lipid Nanoparticles for the Tumor-Specific Activation of Signal Amplification in miRNA Imaging. Angew Chem Int Ed Engl 2022; 61:e202214230. [PMID: 36383756 DOI: 10.1002/anie.202214230] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Indexed: 11/17/2022]
Abstract
MicroRNA (miRNA) imaging in disease sites is vital to elucidate their role in cancer progression. However, limited tumor specificity remains a major barrier for traditional amplification approaches due to associated background signal leakage. Here, we report a generalizable approach via the combination of enzymatically triggered catalytic hairpin assembly with lipid nanoparticles (LNPs)-based delivery strategy for tumor-specific activation of signal amplification and therefore sensitive miRNA imaging. The signal amplification is established via engineering of traditional catalytic hairpin assembly with enzymatically activated motifs to achieve triggable miRNA imaging in cancer cells. Furthermore, by the introduction of LNPs to combat biological barriers, we demonstrate that the system enables amplified miRNA imaging in vivo with reduced off-tumor signal, leading to enhanced tumor-to-background contrast compared with traditional methods. This approach that relies on specific triggers and controlled delivery to distinguish miRNA in cancer cells from normal cells should be useful in tumor diagnosis.
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Affiliation(s)
- Qing Liu
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Yuanyu Huang
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Zhengping Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
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33
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Yang Z, Liu B, Huang T, Sun M, Tong li, Duan WJ, Li MM, Chen JX, Dai Z, Chen J. A domino-like localized cascade toehold assembly amplification-based DNA nanowire for microRNA imaging in living cells. Chem Sci 2022; 13:14373-14381. [PMID: 36545151 PMCID: PMC9749110 DOI: 10.1039/d2sc05890a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022] Open
Abstract
High sensitivity and specificity imaging of miRNA in living cells plays an important role in understanding miRNA-related regulation and pathological research. Localized DNA circuits have shown good performance in reaction rate and sensitivity and have been proposed for sensitive imaging of miRNA in living cells. However, most reported localized DNA circuits have a high risk of derailment or a limited loading rate capacity, which hinder their further application. To solve these issues, we herein developed a domino-like localized cascade toehold assembly (LCTA) amplification-based DNA nanowire to achieve highly sensitive and highly specific imaging of miRNAs in living cells by using DNA nanowires as reactant delivery vehicles and confining both reactant probes in a compact space. The LCTA is constructed by interval hybridization of DNA double-stranded probe pairs to a DNA nanowire with multiplex footholds generated by alternating chain hybridization. Due to the localized effect, the LCTA showed high reaction kinetics and sensitivity, and the method could detect miRNAs as low as 51 pM. The LCTA was proven to be able to accurately distinguish the miRNA expression difference between normal cells and cancer cells. In particular, the developed LCTA could be used to construct an OR logic gate to simultaneously image the total amount of multiple miRNAs in living cells. We believe that the developed LCTA can be an effective intracellular nucleic acid imaging tool and can promote the development of nucleic acid-related clinical disease diagnosis and DNA logical sensors.
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Affiliation(s)
- Zizhong Yang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhou510515P. R. China
| | - Birong Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhou510515P. R. China
| | - Ting Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhou510515P. R. China
| | - Mengxu Sun
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhou510515P. R. China
| | - Tong li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhou510515P. R. China
| | - Wen-Jun Duan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhou510515P. R. China
| | - Min-Min Li
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan UniversityGuangzhou 510632P.R. China
| | - Jin-Xiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhou510515P. R. China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen UniversityShenzhen 518107P. R. China
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical UniversityGuangzhou510515P. R. China
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34
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Zhang J, Lu Y, Gao W, Yang P, Cheng N, Jin Y, Chen J. Structure-switching locked hairpin triggered rolling circle amplification for ochratoxin A (OTA) detection by ICP-MS. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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35
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Liu Q, Huang Y, Li Z, Li L, Zhao Y, Li M. An Enzymatically Gated Catalytic Hairpin Assembly Delivered by Lipid Nanoparticles for the Tumor‐Specific Activation of Signal Amplification in miRNA Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202214230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Qing Liu
- Advanced Research Institute of Multidisciplinary Science School of Life Science Beijing Institute of Technology Beijing 100081 China
| | - Yuanyu Huang
- Advanced Research Institute of Multidisciplinary Science School of Life Science Beijing Institute of Technology Beijing 100081 China
| | - Zhengping Li
- School of Chemistry and Biological Engineering University of Science and Technology Beijing Beijing 100083 China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology Beijing 100190 China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety National Center for Nanoscience and Technology Beijing 100190 China
| | - Mengyuan Li
- School of Chemistry and Biological Engineering University of Science and Technology Beijing Beijing 100083 China
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36
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Wen Y, Zhang XW, Li YY, Chen S, Yu YL, Wang JH. Ultramultiplex NaLnF 4 Nanosatellites Combined with ICP-MS for Exosomal Multi-miRNA Analysis and Cancer Classification. Anal Chem 2022; 94:16196-16203. [DOI: 10.1021/acs.analchem.2c03727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Yun Wen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Xue-Wei Zhang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yuan-Yuan Li
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Shuai Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang 110819, China
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37
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Toehold-mediated biosensors: Types, mechanisms and biosensing strategies. Biosens Bioelectron 2022; 220:114922. [DOI: 10.1016/j.bios.2022.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
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38
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Wang X, Qin Y, Huang Y, Hu K, Zhao S, Tian J. A sensitive and facile microRNA detection based on CRISPR-Cas12a coupled with strand displacement amplification. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 279:121476. [PMID: 35691167 DOI: 10.1016/j.saa.2022.121476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are important biomarkers that are closely associated with certain diseases. The detection of miRNA is critical because it provides the necessary information for Disease Diagnosis. In this study, we achieved miRNA determination by coupling the CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR-associated) system with strand displacement amplification (SDA). In the experiment, miRNA was used as the initiator of SDA, and the activator of Cas12a nuclease activity was amplified by SDA. Subsequently, the unique nuclease activity of Cas12a was exploited to carry out trans cleaving on the ssDNA reporting probe modified with carboxyfluorescein(FAM) and BHQ1(dark Quencher: 480-580 nm) to achieve a signal output. In addition to chain design and reaction simplification, this method is lofty sensitive and selective for the determination of miRNA with a good linear range of 250 fmol·L-1 ∼ 40 pmol·L-1, the detection limit of 150 fmol·L-1 (S/N = 3), and the method showed good recovery in spiked human serum. Overall, this method is expected to be applied to diagnosis with miRNA biomarkers because of its rapidity, high sensitivity, and high selectivity.
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Affiliation(s)
- Xin Wang
- School of Chemistry and Pharmaceutical Science of Guangxi Normal University, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guilin 541004, China
| | - Yuxin Qin
- School of Chemistry and Pharmaceutical Science of Guangxi Normal University, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guilin 541004, China
| | - Yong Huang
- School of Chemistry and Pharmaceutical Science of Guangxi Normal University, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guilin 541004, China
| | - Kun Hu
- School of Chemistry and Pharmaceutical Science of Guangxi Normal University, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guilin 541004, China
| | - Shulin Zhao
- School of Chemistry and Pharmaceutical Science of Guangxi Normal University, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guilin 541004, China
| | - Jianniao Tian
- School of Chemistry and Pharmaceutical Science of Guangxi Normal University, State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guilin 541004, China.
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39
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Chen F, Xue J, Bai M, Fan C, Zhao Y. Lighting Up Nucleic Acid Modifications in Single Cells with DNA-Encoded Amplification. Acc Chem Res 2022; 55:2248-2259. [PMID: 35904502 DOI: 10.1021/acs.accounts.2c00269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleic acids are naturally decorated with various chemical modifications at nucleobases. Most nucleic acid modifications (NAMs) do not alter Watson-Crick base pairing but can regulate gene expression known as "epigenetics". Their abundances present a very wide range, approximately 10-2 to 10-6 of total bases. Different NAMs may coexist in spatial proximity (e.g., <20 nm) in the crowded intracellular environment. Considering the highly dynamic chromatin accessibility (physical access to DNA), the NAMs in inaccessible DNA probably plays different roles. These multilayered features of NAMs vary from cell to cell. Our understanding of the function and mechanism of NAMs in biological processes and disease states has largely been driven by the expanding array of sequencing-based methodologies. However, an underexplored aspect is the measurement of the subcellular distribution, spatial proximity, and inaccessibility of NAMs in single cells. In recent years, we have developed new approaches that light up single-cell NAMs with single-site sensitivity. These methods are mainly based on the integration of chemical or chemoenzymatic tools, DNA amplification and nanotechnology, and/or microfluidics. An overview of these methods together with conventional methods such as immunofluorescence (IF) and fluorescence in situ hybridization (FISH) is provided in this Account.Our laboratory has proposed DNA-encoded amplification (DEA) as the main strategy for developing a set of single-cell NAM imaging methods. In brief, DEA transforms the different features of NAMs into unique DNA primers for rolling circle amplification (RCA) followed by FISH imaging. The first method is base-encoded amplifying FISH (BEA-FISH), in which we convert individual NAMs into RCA primers via chemoselective labeling and click bioconjugation. It enables the in situ visualization of low-abundance NAMs (e.g., 5hmU), which is impracticable by conventional methods. We subsequently developed pairwise proximity-differentiated amplifying FISH (PPDA-FISH), which integrates BEA-FISH with DNA nanotechnology. PPDA-FISH utilizes proximity ligation and toehold strand displacement to label the adjacent site of two different NAMs (one-to-one proximity) and their respective residual sites with three unique RCA probes. It achieves simultaneous counting of the above-mentioned three types of modified sites in the same cells. The third method is cellular macromolecule-tethered DNA walking indexing (Cell-TALKING) to probe more than two NAMs within the same nanoenvironments. Cell-TALKING uses dynamic DNA proximity cleavage to continuously activate different preblocked RCA primers (for each NAM) near one walking probe (for one target molecule). We have explored three NAMs around one histone (one-to-many proximity) in different cancer cell lines and clinical specimens. Then, we describe a single-cell hydrogel encoding amplification (scHEA) method by integrating droplet microfluidics with BEA-FISH. This method generates hydrogel beads that encapsulate single cells and their genomic DNA after cell lysis. It realizes the analysis of global (accessible and inaccessible) DNA from the same cells. We find that the global levels of both 5hmC and 5hmU in single cells can distinguish different breast cancer cells. Finally, the current limitations of these strategies and the future development directions are also discussed. We hope that this Account can spark new ideas and invite new efforts from different disciplines for single-cell NAM analysis.
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Affiliation(s)
- Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
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40
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Wang Y, Feng H, Huang K, Quan J, Yu F, Liu X, Jiang H, Wang X. Target-triggered hybridization chain reaction for ultrasensitive dual-signal miRNA detection. Biosens Bioelectron 2022; 215:114572. [PMID: 35853324 DOI: 10.1016/j.bios.2022.114572] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/29/2022] [Accepted: 07/10/2022] [Indexed: 12/12/2022]
Abstract
A signal amplification sensing system with target-triggered DNA cascade reaction combined with dual-signal readout technology was designed for ultrasensitive analysis of miRNA. The highly conductive metal organic frameworks (MOFs) derivative, N-doped carbon dodecahedron (N-PCD) was deposited with gold nanoparticles as the electrode substrate, which could assist the electron transfer between the molecular probe and the electrode surface, and could remarkably enhance electrochemical response. Tetrahedral DNA nanostructure (T4-DNA) with high structural stability and mechanical stiffness was designed to improve the loading capacity and binding efficiency of the target, thus increasing the sensitivity of the system. The non-enzymatic amplification method based on the DNA cascade reaction allows the electrochemical responses from dual signal DNA probes labeled with ferrocene (Fc) and methylene blue (MB), respectively in turn to improve the reliability of detection. Under optimal conditions, the sensor has a linear range of 5-1.0 × 104 fM, and the limit of detection is as low as 1.92 fM and 3.74 fM for Fc and MB labeled probe, respectively. This strategy raises the promising application for the rapid detection of miRNA targets with low abundance in complex biological systems.
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Affiliation(s)
- Yihan Wang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Huan Feng
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Ke Huang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Jinfeng Quan
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Fangfang Yu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xiaohui Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Hui Jiang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
| | - Xuemei Wang
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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41
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Zhang Y, Chen J, Yang H, Yin W, Li C, Xu Y, Liu SY, Dai Z, Zou X. Light-Controlled Recruitable Hybridization Chain Reaction on Exosome Vehicles for Highly Sensitive MicroRNA Imaging in Living Cells. Anal Chem 2022; 94:9665-9673. [PMID: 35758600 DOI: 10.1021/acs.analchem.2c00974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Sensitive imaging of intracellular microRNA (miRNA) in living cells is of great significance. Isothermal hybridization chain reaction (HCR)-based methods, although have been widely used to monitor intracellular low-abundance miRNA, are still subjected to the challenges of limited signal amplification efficiency and compromised imaging resolution. In this work, we design a light-controlled recruitable HCR (LCR-HCR) strategy that enables us to well overcome these limitations. Exosomes as delivery and recruitment vehicles are modified with three cholesterol-modified hairpins (H1, H2, and H3), in which H1 is for anchoring target miRNA and H2 and H3 with photocleavable linkers (PC-linkers) are designed for spatiotemporal HCR. By controllably releasing probes with high local concentrations to efficiently trigger HCR and further recruiting the generated double-stranded DNA (dsDNA) polymers instead of dispersion in the cytoplasm, the LCR-HCR method can significantly improve the imaging contrast by confining all of the reactants on exosome vehicles. For a proof-of-concept demonstration, the miR-21 was analyzed by LCR-HCR with a limit of detection (LOD) down to 3.3 pM (corresponding to 165 amol per 50 μL) in vitro and four times higher response than traditional HCR in vivo. In general, the LCR-HCR method provides a powerful tool for sensitive miRNA imaging in living cells and cancer diagnosis.
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Affiliation(s)
- Yanfei Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huihui Yang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wen Yin
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chunrong Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuzhi Xu
- Scientific Research Center, Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen 518107, China
| | - Si-Yang Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Xiaoyong Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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42
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Wang Q, Xiao F, Su H, Liu H, Xu J, Tang H, Qin S, Fang Z, Lu Z, Wu J, Weng X, Zhou X. Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells. Nucleic Acids Res 2022; 50:e84. [PMID: 35580055 PMCID: PMC9371900 DOI: 10.1093/nar/gkac368] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/01/2022] [Accepted: 05/12/2022] [Indexed: 02/06/2023] Open
Abstract
The development of RNA aptamers/fluorophores system is highly desirable for understanding the dynamic molecular biology of RNAs in vivo. Peppers-based imaging systems have been reported and applied for mRNA imaging in living cells. However, the need to insert corresponding RNA aptamer sequences into target RNAs and relatively low fluorescence signal limit its application in endogenous mRNA imaging. Herein, we remolded the original Pepper aptamer and developed a tandem array of inert Pepper (iPepper) fluorescence turn-on system. iPepper allows for efficient and selective imaging of diverse endogenous mRNA species in live cells with minimal agitation of the target mRNAs. We believe iPepper would significantly expand the applications of the aptamer/fluorophore system in endogenous mRNA imaging, and it has the potential to become a powerful tool for real-time studies in living cells and biological processing.
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Affiliation(s)
- Qi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Hui Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Heng Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Zhentian Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jian Wu
- School of Medicine, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,The Institute of Advanced Studies, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
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43
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Teng X, Dai Y, Li J. Module Assembly Strategy for Single‐Cell Nucleic Acid Imaging at the Sub‐Molecule Level. Chemistry 2022; 28:e202104628. [DOI: 10.1002/chem.202104628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Indexed: 11/11/2022]
Affiliation(s)
- Xucong Teng
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University 100084 Beijing P. R. China
| | - Yicong Dai
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University 100084 Beijing P. R. China
| | - Jinghong Li
- Department of Chemistry Center for BioAnalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology Tsinghua University 100084 Beijing P. R. China
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44
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Wang H, He Y, Wei J, Wang H, Ma K, Zhou Y, Liu X, Zhou X, Wang F. Construction of an Autocatalytic Hybridization Assembly Circuit for Amplified In Vivo MicroRNA Imaging. Angew Chem Int Ed Engl 2022; 61:e202115489. [PMID: 35076991 DOI: 10.1002/anie.202115489] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 12/15/2022]
Abstract
Lowly expressed analyte in complex cytoplasmic milieu necessitates the development of non-enzymatic autocatalytic DNA circuits with high amplification and anti-interference performance. Herein, we engineered a versatile and robust stimuli-responsive autocatalytic hybridization assembly (AHA) circuit for high-performance in vivo bioanalysis. Under a moderately confined condition, the initiator motivated the autonomous and cooperative cross-activation of cascade hybridization reaction and catalytic DNA assembly for generating an exponentially amplified readout without the parasite steric hindrance and random diffusion side effects. The AHA circuit was systematically investigated by a series of experimental studies and theoretical simulations. The successively guaranteed target recognition and synergistically accelerated signal-amplification enabled the sensitive and selective detection of analyte, and realized the robust miRNA imaging in living cells and mice. This autocatalytic DNA circuit could substantially expand the toolbox for accurate diagnosis and programmable therapeutics.
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Affiliation(s)
- Huimin Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China.,College of Biological and Pharmaceutical Sciences, China Three Gorges University, 443002, Yichang, P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Jie Wei
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Hong Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Kang Ma
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Yangjie Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, 430072, Wuhan, P. R. China
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45
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Xia X, Yang H, Cao J, Zhang J, He Q, Deng R. Isothermal nucleic acid amplification for food safety analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116641] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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46
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Xue C, Niu H, Hu S, Yang Z, Wang L, Wu ZS. Visually predicting microRNA-regulated tumor metastasis by intracellularly 3D counting of fluorescent spots based on in situ growth of DNA flares. J Adv Res 2022; 43:73-85. [PMID: 36585116 PMCID: PMC9811323 DOI: 10.1016/j.jare.2022.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/02/2022] [Accepted: 03/01/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION MicroRNAs (miRNAs) have been revealed to be critical genetic regulators in various physiological processes and thus quantitative information on the expression level of critical miRNAs has important implications for the initiation and development of human diseases, including cancers. OBJECTIVES We herein develop three-dimensionally (3D) counting of intracellular fluorescent spots for accurately evaluating microRNA-21 (miRNA-21) expression in individual HeLa cells based on stimuli-activated in situ growth of optical DNA flares, grid-patterned DNA-protein hybrids (GDPHs). METHODS Target miRNA is sequence-specifically detected down to 10 pM owing to efficient signal amplification. Within living cells, GDPH flares are nuclease resistant and discrete objects with retarded mobility, enabling the screening of intracellular location and distribution of miRNAs and realizing in situ counting of target species with a high accuracy. RESULTS The quantitative results of intracellular miRNAs by 3D fluorescence counts are consistent with qPCR gold standard assay, exhibiting the superiority over 2D counts. By screening the expression of intracellular miR-21 that can down-regulate the programmed cell death 4 (PDCD4) protein, the proliferation and migration of HeLa cells, including artificially-regulated ones, were well estimated, thus enabling the prediction of cancer metastasis in murine tumor models. CONCLUSION The experiments in vitro, ex vivo and in vivo demonstrate that GDPH-based 3D fluorescence counts at the single cell level provide a valuable molecular tool for understanding biological function of miRNAs and especially for recognizing aggressive CTCs, offering a design blueprint for further expansion of DNA structural nanotechnology in predicting distant metastasis and prevention of tumor recurrence after primary resection.
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Affiliation(s)
- Chang Xue
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Huimin Niu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China,Fujian Key Laboratory of Aptamers Technology, The 900 Hospital of Joint Logistics Support Force, Fuzhou 350025, China
| | - Shuyao Hu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zhe Yang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Lei Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China,Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China,Corresponding author.
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47
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Zhu Y, Wang J, Xie H, Liu H, Liu S, He D, Mi P, He S, Wang J, Sun Y. NIR-to-Vis Handheld Platforms for Detecting miRNA Level and Mutation Based on Sub-10 nm Sulfide Nanodots and HCR Amplification. ACS APPLIED MATERIALS & INTERFACES 2022; 14:10212-10226. [PMID: 35188756 DOI: 10.1021/acsami.2c00689] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Sub-10 nm monodisperse alkaline-earth sulfide nanodots (ASNDs) with bright near-infrared (NIR)-excitation fluorescence and adjustable emission wavelength were prepared by a thermal decomposition method for the first time. The ASNDs exhibited high NIR-to-vis conversion efficiency and served as multicolor fluorescent labels in the proposed miR-224 assay. Targeted detection of the miR-224 level and single-nucleotide variation in miR-224 was carried out on a smartphone-based platform using a hybridization chain reaction (HCR) amplification strategy. In the presence of miR-224, the ASND-labeled HCR probes self-assembled on the surface of the diagnosis kits, generating strong fluorescent signals linearly proportional to miR-224 contents in the range of 10-2000 fM. Significantly, mutations in miR-224 led to the variation in the fluorescence intensity ratio in RGB channels. Simultaneously, evident changes of fluorescent brightness and color were easily visualized by the naked eye, which enabled on-site discrimination of miR-224 with different mutant loci. This work provides a novel preparation approach for ultrasmall NIR excitation sulfide nanodots and reveals the potential of the as-synthesized ASNDs in point-of-care (POC) nucleic acid testing. Further, it may provide a handheld platform for miRNA single-nucleotide polymorphism analysis.
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Affiliation(s)
- Yanli Zhu
- School of Resources and Environment, Hunan University of Technology and Business, Changsha 410205, Hunan, P. R. China
| | - Jikai Wang
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy & Pharmacology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, P. R. China
| | - Haitao Xie
- Department of Clinical Laboratory, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, P. R. China
| | - Hailing Liu
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, P. R. China
| | - Shuangquan Liu
- Department of Clinical Laboratory, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, P. R. China
| | - Dongxiu He
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy & Pharmacology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, P. R. China
| | - Pengbing Mi
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy & Pharmacology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, P. R. China
| | - Suisui He
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy & Pharmacology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, P. R. China
| | - Jun Wang
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy & Pharmacology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, P. R. China
| | - Yiyang Sun
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Institute of Pharmacy & Pharmacology, Hengyang Medical School, University of South China, Hengyang 421001, Hunan, P. R. China
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48
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Wang H, He Y, Wei J, Wang H, Ma K, Zhou Y, Liu X, Zhou X, Wang F. Construction of an Autocatalytic Hybridization Assembly Circuit for Amplified
In Vivo
MicroRNA Imaging. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Huimin Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
- College of Biological and Pharmaceutical Sciences China Three Gorges University 443002 Yichang P. R. China
| | - Yuqiu He
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Jie Wei
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Hong Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Kang Ma
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Yangjie Zhou
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences Wuhan University 430072 Wuhan P. R. China
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49
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Liu Y, Li B, Wang YJ, Fan Z, Du Y, Li B, Liu YJ, Liu B. In Situ Single-Molecule Imaging of MicroRNAs in Switchable Migrating Cells under Biomimetic Confinement. Anal Chem 2022; 94:4030-4038. [PMID: 35213802 DOI: 10.1021/acs.analchem.1c05223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Spatial imaging of RNAs in single cells is extremely charming for deciphering of regulatory mechanisms in multiple migration modes during tumor metastasis. Herein, enzyme-free-mediated cascade amplified nanoprobes were designed for in situ single-molecule imaging of dual-microRNAs (miRNAs) in switchable migrating cells. Differential expression and localization of dual-miRNAs were clearly exhibited in multiple cell lines attributed to enhanced sensitivity via the cascade signal amplification strategy. Significantly, in situ three-dimensional (3D) imaging of dual-miRNAs in transition of cell migration phenotypes was successfully reconstructed in both non-confined and confined microenvironments in vitro, of which differential spatial distribution was observed in a single cell. This is very promising for exploring key roles of spatial RNA distribution in migrating cells at the single-molecule level, which will advance revealing the molecular mechanism and physical principle in 3D cell migration in vivo.
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Affiliation(s)
- Yixin Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Binxiao Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Ya-Jun Wang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Zihui Fan
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Yang Du
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Bin Li
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Yan-Jun Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Lab of Molecular Engineering of Polymers, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences Fudan University, Shanghai 200433, China
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50
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Zhang P, Ouyang Y, Sohn YS, Fadeev M, Karmi O, Nechushtai R, Stein I, Pikarsky E, Willner I. miRNA-Guided Imaging and Photodynamic Therapy Treatment of Cancer Cells Using Zn(II)-Protoporphyrin IX-Loaded Metal-Organic Framework Nanoparticles. ACS NANO 2022; 16:1791-1801. [PMID: 35020370 PMCID: PMC8867907 DOI: 10.1021/acsnano.1c04681] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
An analytical platform for the selective miRNA-21-guided imaging of breast cancer cells and miRNA-221-guided imaging of ovarian cancer cells and the selective photodynamic therapy (PDT) of these cancer cells is introduced. The method is based on Zn(II)-protoporphyrin IX, Zn(II)-PPIX-loaded UiO-66 metal-organic framework nanoparticles, NMOFs, gated by two hairpins Hi/Hj through ligation of their phosphate residues to the vacant Zr4+-ions associated with the NMOFs. The hairpins are engineered to include the miRNA recognition sequence in the stem domain of Hi, and in the Hi and Hj, partial locked stem regions of G-quadruplex subunits. Intracellular phosphate-ions displace the hairpins, resulting in the release of the Zn(II)-PPIX and intracellular miRNAs open Hi, and this triggers the autonomous cross-opening of Hi and Hj. This activates the interhairpin hybridization chain reaction and leads to the assembly of highly fluorescent Zn(II)-PPIX-loaded G-quadruplex chains. The miRNA-guided fluorescent chains allow selective imaging of cancer cells. Moreover, PDT with visible light selectively kills cancer cells and tumor cells through the formation of toxic reactive oxygen species.
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Affiliation(s)
- Pu Zhang
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yu Ouyang
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yang Sung Sohn
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Michael Fadeev
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ola Karmi
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Rachel Nechushtai
- Institute
of Life Science, The Hebrew University of
Jerusalem, Jerusalem 91904, Israel
| | - Ilan Stein
- The
Lautenberg Center for Immunology and Cancer Research, IMRIC, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Eli Pikarsky
- The
Lautenberg Center for Immunology and Cancer Research, IMRIC, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Itamar Willner
- Institute
of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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