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Zeng H, Zhou H, Lin J, Pang Q, Chen S, Lin S, Xue C, Shen Z. Palindrome-Embedded Hairpin Structure and Its Target-Catalyzed Padlock Cyclization for Label-Free MicroRNA-Initiated Rolling Circle Amplification. ACS OMEGA 2023; 8:2253-2261. [PMID: 36687024 PMCID: PMC9850459 DOI: 10.1021/acsomega.2c06532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Highly sensitive detection of microRNAs (miRNAs) is of great significance in early diagnosis of cancers. Here, we develop a palindrome-embedded hairpin structure and its target-catalyzed padlock cyclization for rolling circle amplification, named PHP-RCA for simplicity, which can be applied in label-free ultrasensitive detection of miRNA. PHP-RCA is a facile system that consists of only an oligonucleotide probe with a palindrome-embedded hairpin structure (PHP). The two ends of PHP were extended as overhangs and designed with the complementary sequences of the target. Hence, the phosphorylated PHP can be cyclized by T4 DNA ligase in the presence of the target that serves as the ligation template. This ligation has formed a palindrome-embedded dumbbell-shaped probe (PDP) that allows phi29 polymerase to perform a typical target-primed RCA on PDP by taking miRNA as a primer, resulting in the production of a lengthy tandem repeat. Benefits from the palindromic sequences and hairpin-shaped structure in padlock double-stranded structures can be infinitely produced during the RCA reaction and provide numerous binding sites for SYBR Green I, a double-stranded dye, achieving a sharp response signal for label-free target detection. We have demonstrated that the proposed system exhibits a good linear range from 0.1 fM to 5 nM with a low detection limit of 0.1 fM, and the non-target miRNA can be clearly distinguished. The advantages of high efficiency, label-free signaling, and the use of only one oligonucleotide component make the PHP-RCA suitable for ultrasensitive, economic, and convenient detection of target miRNAs. This simple and powerful system is expected to provide a promising platform for tumor diagnosis, prognosis, and therapy.
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Affiliation(s)
- Huaiwen Zeng
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Hongyin Zhou
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
| | - Junliang Lin
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Qi Pang
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Siqiang Chen
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Shaoqi Lin
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Chang Xue
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
| | - Zhifa Shen
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
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2
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Liang Z, Chen M, Huang X, Tong Y, Wang Q, Chen Z. Integration of exonuclease III-assisted recycling amplification and multi-site enzyme polymerization labeling for sensitive detection of p53 gene. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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3
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Tavakoli J, Wang J, Chuah C, Tang Y. Natural-based Hydrogels: A Journey from Simple to Smart Networks for Medical Examination. Curr Med Chem 2020; 27:2704-2733. [PMID: 31418656 DOI: 10.2174/0929867326666190816125144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Natural hydrogels, due to their unique biological properties, have been used extensively for various medical and clinical examinations that are performed to investigate the signs of disease. Recently, complex-crosslinking strategies improved the mechanical properties and advanced approaches have resulted in the introduction of naturally derived hydrogels that exhibit high biocompatibility, with shape memory and self-healing characteristics. Moreover, the creation of self-assembled natural hydrogels under physiological conditions has provided the opportunity to engineer fine-tuning properties. To highlight recent studies of natural-based hydrogels and their applications for medical investigation, a critical review was undertaken using published papers from the Science Direct database. This review presents different natural-based hydrogels (natural, natural-synthetic hybrid and complex-crosslinked hydrogels), their historical evolution, and recent studies of medical examination applications. The application of natural-based hydrogels in the design and fabrication of biosensors, catheters and medical electrodes, detection of cancer, targeted delivery of imaging compounds (bioimaging) and fabrication of fluorescent bioprobes is summarised here. Without doubt, in future, more useful and practical concepts will be derived to identify natural-based hydrogels for a wide range of clinical examination applications.
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Affiliation(s)
- Javad Tavakoli
- Institute of NanoScale Science and Technology, Medical Device Research Institute, College of Science and Engineering, Flinders University, South Australia 5042, Australia.,School of Biomedical Engineering, University of Technology Sydney, Ultimo, 2007 NSW, Australia
| | - Jing Wang
- Institute of NanoScale Science and Technology, Medical Device Research Institute, College of Science and Engineering, Flinders University, South Australia 5042, Australia.,Key Laboratory of Advanced Textile Composite Materials of Ministry of Education, Institute of Textile Composite, School of Textile, Tianjin Polytechnic University, Tianjin 300387, China
| | - Clarence Chuah
- Institute of NanoScale Science and Technology, Medical Device Research Institute, College of Science and Engineering, Flinders University, South Australia 5042, Australia
| | - Youhong Tang
- Institute of NanoScale Science and Technology, Medical Device Research Institute, College of Science and Engineering, Flinders University, South Australia 5042, Australia
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4
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Kim DM, Yoo SM. DNA-modifying enzyme reaction-based biosensors for disease diagnostics: recent biotechnological advances and future perspectives. Crit Rev Biotechnol 2020; 40:787-803. [DOI: 10.1080/07388551.2020.1764485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Dong Min Kim
- Center for Applied Life Science, Hanbat National University, Daejeon, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
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5
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Pirzada M, Altintas Z. Nanomaterials for Healthcare Biosensing Applications. SENSORS (BASEL, SWITZERLAND) 2019; 19:E5311. [PMID: 31810313 PMCID: PMC6928990 DOI: 10.3390/s19235311] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
Abstract
In recent years, an increasing number of nanomaterials have been explored for their applications in biomedical diagnostics, making their applications in healthcare biosensing a rapidly evolving field. Nanomaterials introduce versatility to the sensing platforms and may even allow mobility between different detection mechanisms. The prospect of a combination of different nanomaterials allows an exploitation of their synergistic additive and novel properties for sensor development. This paper covers more than 290 research works since 2015, elaborating the diverse roles played by various nanomaterials in the biosensing field. Hence, we provide a comprehensive review of the healthcare sensing applications of nanomaterials, covering carbon allotrope-based, inorganic, and organic nanomaterials. These sensing systems are able to detect a wide variety of clinically relevant molecules, like nucleic acids, viruses, bacteria, cancer antigens, pharmaceuticals and narcotic drugs, toxins, contaminants, as well as entire cells in various sensing media, ranging from buffers to more complex environments such as urine, blood or sputum. Thus, the latest advancements reviewed in this paper hold tremendous potential for the application of nanomaterials in the early screening of diseases and point-of-care testing.
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Affiliation(s)
| | - Zeynep Altintas
- Technical University of Berlin, Straße des 17. Juni 124, 10623 Berlin, Germany;
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6
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Su D, Li N, Liu Y, Wang M, Su X. Ratiometric fluorescence strategy for p53 gene assay by using nitrogen doped graphene quantum dots and berberine as fluorescence reporters. Anal Chim Acta 2019; 1084:78-84. [DOI: 10.1016/j.aca.2019.07.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 01/10/2023]
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7
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Ultrasensitive assay based on a combined cascade amplification by nicking-mediated rolling circle amplification and symmetric strand-displacement amplification. Anal Chim Acta 2019; 1047:172-178. [DOI: 10.1016/j.aca.2018.10.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/31/2018] [Accepted: 10/03/2018] [Indexed: 01/05/2023]
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8
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Xue C, Xiao S, Ouyang CH, Li CC, Gao ZH, Shen ZF, Wu ZS. Inverted mirror image molecular beacon-based three concatenated logic gates to detect p53 tumor suppressor gene. Anal Chim Acta 2018; 1051:179-186. [PMID: 30661615 DOI: 10.1016/j.aca.2018.11.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/29/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022]
Abstract
Mutation of p53 tumor suppressor gene represents one of the early molecular events in tumor initiation and progression. Although molecular computing holds tremendous potential with important applications in diagnosis, prognosis and treatment of human diseases at the molecular level, designing molecular logic gates to implement cascade amplification via operating autonomously for the detection of point mutations still remains challenging. In this contribution, we developed a three concatenated logic gates (TCLG) to perform multiple strand displacement amplification (m-SDA) for screening the cancer-related point mutations only via designing an innovative molecular beacon (MB). Specifically, using p53 gene as model target, extending the two ends of a MB via adding two fragments with the same sequence achieves two unique terminal single-stranded (ss) overhangs. After self-folding of MB into hairpin structure, the two overhangs exhibit a near inverted mirror image (IM) relationship if taking the base nature and direction into account. For this, the probe is called IM-MB. Because cascade SDAs can occur on IM-MB and promote each other, the target gene can be detected down to 10 pM. Along this line, the TCLG circuit was proposed, and two primers and target gene serve as the indispensable input signals. Utilizing this logic circuit, the point mutation or absence of target gene can be sensitively screened. Moreover, its potential application in the recognition of point mutations in complex biomatrix has been demonstrated via blind test. The proof-of-concept scheme is expected to provide new insight into the development of DNA-based molecular logic gates and their applications in basic research, medical diagnosis and precise treatment and treatment of genetic diseases.
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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, 350002, China
| | - Shuai Xiao
- 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, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Chang-He Ouyang
- 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, 350002, China
| | - Cong-Cong Li
- 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, 350002, China
| | - Zhi-Hua Gao
- 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, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhi-Fa Shen
- 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, 350002, China; Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou, 325035, 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, 350002, China.
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A star-shaped DNA probe based on strand displacement for universal and multiplexed fluorometric detection of genetic variations. Mikrochim Acta 2018; 185:413. [DOI: 10.1007/s00604-018-2941-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022]
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10
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Cui Y, Han X, An R, Zhou G, Komiyama M, Liang X. Cyclization of secondarily structured oligonucleotides to single-stranded rings by using Taq DNA ligase at high temperatures. RSC Adv 2018; 8:18972-18979. [PMID: 35539641 PMCID: PMC9080623 DOI: 10.1039/c8ra02804d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 05/10/2018] [Indexed: 11/21/2022] Open
Abstract
Single-stranded DNA rings play important roles in nanoarchitectures, molecular machines, DNA detection, etc. Although T4 DNA ligase has been widely employed to cyclize single-stranded oligonucleotides into rings, the cyclization efficiency is very low when the oligonucleotides (l-DNAs) take complicated secondary structures at ambient temperatures. In the present study, this problem has been solved by using Thermus aquaticus DNA ligase (Taq DNA ligase) at higher temperatures (65 and 70 °C) where the secondary structures are less stable or completely destroyed. This method is based on our new finding that this ligase successfully functions even when the splint strand is short and forms no stable duplex with l-DNA (at least in the absence of the enzyme). In order to increase the efficiency of cyclization, various operation factors (lengths and sequences of splint, as well as the size of the DNA ring) have been investigated. Based on these results, DNA rings have been successfully synthesized from secondarily structured oligonucleotides in high yields and high selectivity. The present methodology is applicable to the preparation of versatile DNA rings involving complicated secondary structures, which should show novel properties and greatly widen the scope of DNA-based nanotechnology. We have achieved the efficient preparation of single-stranded DNA rings from secondarily structured oligonucleotides.![]()
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Affiliation(s)
- Yixiao Cui
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Xutiange Han
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Ran An
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
| | - Guangqing Zhou
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
| | - Makoto Komiyama
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- National Institute for Materials Science (NIMS)
| | - Xingguo Liang
- College of Food Science and Engineering
- Ocean University of China
- Qingdao 266003
- China
- Laboratory for Marine Drugs and Bioproducts
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