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Lv F, Chen J, Wan Y, Si J, Song M, Zhu F, Du S, Shang Y, Man T, Zhu L, Ren K, Piao Y, Zhu C, Deng SY. Amplification of an Electrochemiluminescence-Emissive Aptamer into DNA Nanotags for Sensitive Fecal Calprotectin Determination. Anal Chem 2023; 95:18564-18571. [PMID: 38060825 DOI: 10.1021/acs.analchem.3c04390] [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: 12/20/2023]
Abstract
The precision additive manufacturing and tessellated multitasking out of the structural DNA nanotechnology enable a configurable expression of densified electrochemiluminescent (ECL) complexes, which would streamline the bioconjugation while multiplying signals. Herein, a completely DNA-scaffold ECL "polyploid" was replicated out via the living course of rolling circle amplification. The amplicon carried the aptameric sequences of ZnPPIX/TSPP porphyrin as photoreactive centers that rallied at periodical intervals of the persistent extension into a close-packed nanoflower, ZnPDFI/II. Both microscopies and electrophoresis proved the robust nesting of guests at their deployed gene loci, while multispectral comparisons among cofactor substituents pinpointed the pivotal roles of singlet seclusion and Zn2+-chelation for the sake of intensive ECL irradiation. The adversity-resilient hydrogel texture made lipoidal filmogens as porphyrinic ECL prerequisites to be of no need at all, thus not only simplifying assay flows but also inspiring an in situ labeling plan. Upon bioprocessing optimization, an enriched probe ZnPDFIII was further derived that interpolated the binding motif related to calprotectin as validated by molecular docking and affinity titration. With it being a strongly indicative marker of inflammatory bowel disease (IBD), a competitive ECL aptasensing strategy was contrived, managing a signal-on and sensitive detection in mild conditions with a subnanogram-per-milliliter limit of detection by 2 orders of magnitude lower than the standard method as well as a comparable accuracy in clinical stool sample testing. Distinct from those conventional chemophysical rebuilding routes, this de novo biosynthetic fusion demonstrated a promising alternative toward ECL-source bioengineering, which may intrigue vibrant explorations of other ECL-shedding fabrics and, accordingly, a new bioanalytic mode downstream.
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Affiliation(s)
- Fujin Lv
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jialiang Chen
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ying Wan
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jingyi Si
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Meiyan Song
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Fulin Zhu
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Songyuan Du
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuzhe Shang
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Tiantian Man
- School of Mechanical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Longyi Zhu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuhao Piao
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Changfeng Zhu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, Nanjing 210023, China
| | - Sheng-Yuan Deng
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
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Zheng X, Gao S, Wu J, Hu X. A Fluorescent Aptasensor Based on Assembled G-Quadruplex and Thioflavin T for the Detection of Biomarker VEGF165. Front Bioeng Biotechnol 2021; 9:764123. [PMID: 34869275 PMCID: PMC8636943 DOI: 10.3389/fbioe.2021.764123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/29/2021] [Indexed: 01/05/2023] Open
Abstract
VEGF165, a regulator of angiogenesis, has been widely used as a serum biomarker for a number of human diseases, including cancer, rheumatoid arthritis, bronchial asthma, and diabetic eye disease. The rapid, accurate, and convenient detection of VEGF165 is a crucial step in effective healthcare monitoring, disease diagnosis, and prognosis assessment. In this study, a fluorescent aptasensor based on an assembled G-quadruplex and the signal molecule ThT was developed for VEGF165 detection. First, G-rich DNA fragments were assembled at both ends of the anti-VEGF165 aptamer, and the B-DNA form was converted into a G-quadruplex structure aptamer (G4-Apt). Then, ThT was introduced, and the G-quadruplex significantly enhanced the fluorescence intensity of the bound ThT. When VEGF165 was present, the higher affinity of the aptamer to the target protein allowed the G4-Apt/VEGF165 complex to form and release ThT, which emitted only weak fluorescence in the free state. Therefore, the aptasensor exhibited a good linear detection window from 1.56 to 25 nM VEGF165, with a limit of detection of 0.138 nM. In addition, the aptasensor was applied to detect VEGF165 in clinical serum samples, showing good accuracy, reproducibility, and stability. These results indicate that our developed fluorescent aptasensor can potentially be a reliable, convenient, and cost-effective approach for the sensitive, specific, and rapid detection of the VEGF165 biomarker.
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Affiliation(s)
- Xin Zheng
- Department of Clinical Laboratory, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shunxiang Gao
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Jihong Wu
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia, Fudan University, Shanghai, China
- Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Xiaobo Hu
- Department of Clinical Laboratory, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Sun L, Tian H, Xue S, Ye H, Xue X, Wang R, Liu Y, Zhang C, Chen Q, Gao S. Circadian Clock Genes REV-ERBs Inhibits Granulosa Cells Apoptosis by Regulating Mitochondrial Biogenesis and Autophagy in Polycystic Ovary Syndrome. Front Cell Dev Biol 2021; 9:658112. [PMID: 34422794 PMCID: PMC8374745 DOI: 10.3389/fcell.2021.658112] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is an endocrinopathy with complex pathophysiology that is a common cause of anovulatory infertility in women. Although the disruption of circadian rhythms is indicated in PCOS, the role of the clock in the etiology of these pathologies has yet to be appreciated. The nuclear receptors REV-ERBα and REV-ERBβ are core modulators of the circadian clock and participate in the regulation of a diverse set of biological functions. However, in PCOS, the expression of REV-ERBs and their effects remain unclear. Here, we demonstrate that the levels of REV-ERBα and REV-ERBβ expression were lower in the granulosa cells of PCOS patients than in control subjects. In vitro, we found that the overexpression of REV-ERBα and REV-ERBβ, and their agonist SR9009, promoted the expression of mitochondrial biosynthesis genes PGC-1α, NRF1, and TFAM and inhibited autophagy in KGN cells. Our results also indicate that REV-ERBα and REV-ERBβ can inhibit apoptosis in granulosa cells and promote proliferation. Importantly, the REV-ERB agonist SR9009 ameliorates abnormal follicular development by promoting mitochondrial biosynthesis and inhibiting autophagy in a mouse PCOS model. This allows us to speculate that SR9009 has potential as a therapeutic agent for the treatment of PCOS.
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Affiliation(s)
- Lihua Sun
- Department of Reproductive Medicine Center, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hui Tian
- Department of Reproductive Medicine Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Songguo Xue
- Department of Reproductive Medicine Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hongjuan Ye
- Department of Reproductive Medicine Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xue Xue
- Department of Reproductive Medicine Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Rongxiang Wang
- Department of Reproductive Medicine Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yu Liu
- Department of Reproductive Medicine Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Caixia Zhang
- Department of Reproductive Medicine Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiuju Chen
- Department of Assisted Reproduction, Shanghai Ninth Peoples Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
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Kandasamy T, Sudhamalla B, Naskar D. Designing of RNA aptamer against DNA binding domain of the glucocorticoid receptor: A response element-based in-silico approach. J Biomol Struct Dyn 2020; 40:1120-1127. [PMID: 32964813 DOI: 10.1080/07391102.2020.1822918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Virtual screening, a conventional in-silico approach to design an RNA aptamer against target proteins require huge RNA library containing 1010 to 1015 combination of RNA oligomers and high-performance computing systems. However, in the case of nuclear receptor proteins, screening can be narrowed down by using response element sequences rather than random RNA oligomer library. In this study, we used a novel method to design RNA aptamer against the DNA binding domain of the glucocorticoid receptor α (GRα). GRα plays a vital role in cancer metastasis such as colon, cervical and breast cancer by activating the S100A8 calcium-binding protein, which makes it a potential drug target for those cancers. We started the screening of 24 RNA aptamers (16 nucleotides long), all of which are glucocorticoid response elements (GRE) of S100A8. Among the aptamers screened, Apt-2, Apt-5, Apt-6 and Apt-15 are found to be most suitable by molecular docking and dynamic studies. The stability and compactness of the aptamer-protein complexes were assessed by GROMACS. The binding energies were rescored using the MM-PBSA method, which were -3679.581, -3690.892, -8246.052 and -3412.802 KJ/mol, respectively for Apt-2, Apt- 5, Apt-6 and Apt-15. The designed RNA aptamer may directly bind to the DNA binding domain of GR and prevent the trans-activation of the S100A8 gene by blocking the binding of GR to its response element. Thus, this novel approach of design the response elements-based RNA aptamer against GRα like nuclear receptor proteins will help to generate target-specific RNA aptamers with minimal efforts and cost.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thirukumaran Kandasamy
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
| | - Babu Sudhamalla
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Debdut Naskar
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, West Bengal, India
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