1
|
He Q, Chen Q, Lian L, Qu J, Yuan X, Wang C, Xu L, Wei J, Zeng S, Yu D, Dong Y, Zhang Y, Deng L, Du K, Zhang C, Pandey V, Gul I, Qin P. Unraveling the influence of CRISPR/Cas13a reaction components on enhancing trans-cleavage activity for ultrasensitive on-chip RNA detection. Mikrochim Acta 2024; 191:466. [PMID: 39017814 DOI: 10.1007/s00604-024-06545-4] [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: 01/17/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024]
Abstract
The CRISPR/Cas13 nucleases have been widely documented for nucleic acid detection. Understanding the intricacies of CRISPR/Cas13's reaction components is pivotal for harnessing its full potential for biosensing applications. Herein, we report on the influence of CRISPR/Cas13a reaction components on its trans-cleavage activity and the development of an on-chip total internal reflection fluorescence microscopy (TIRFM)-powered RNA sensing system. We used SARS-CoV-2 synthetic RNA and pseudovirus as a model system. Our results show that optimizing Mg2+ concentration, reporter length, and crRNA combination significantly improves the detection sensitivity. Under optimized conditions, we detected 100 fM unamplified SARS-CoV-2 synthetic RNA using a microtiter plate reader. To further improve sensitivity and provide a new amplification-free RNA sensing toolbox, we developed a TIRFM-based amplification-free RNA sensing system. We were able to detect RNA down to 100 aM. Furthermore, the TIRM-based detection system developed in this study is 1000-fold more sensitive than the off-coverslip assay. The possible clinical applicability of the system was demonstrated by detecting SARS-CoV-2 pseudovirus RNA. Our proposed sensing system has the potential to detect any target RNA with slight modifications to the existing setup, providing a universal RNA detection platform.
Collapse
Affiliation(s)
- Qian He
- School of Communication Engineering, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
| | - Qun Chen
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
| | - Lijin Lian
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
| | - Jiuxin Qu
- Clinical Laboratory, Shenzhen Third People's Hospital, Shenzhen, 518115, Guangdong Province, China
| | - Xi Yuan
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
| | - Chuhui Wang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
| | - Lidan Xu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jiazhang Wei
- Department of Otolaryngology & Head and Neck, The People's Hospital of Guangxi Zhuang Autonomous Region, Guangxi Academy of Medical Sciences, 6 Taoyuan Road, Nanning, 530021, China
| | - Shaoling Zeng
- Animal and Plant Inspection and Quarantine Technology Center, Shenzhen Customs, Shenzhen, 518010, Guangdong Province, China
| | - Dongmei Yu
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai, 264209, Shandong, China
| | - Yuhan Dong
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
| | - Yongbing Zhang
- Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China
| | - Lin Deng
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Ke Du
- Chemical and Environmental Engineering, University of California, Riverside, USA
| | - Canyang Zhang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
| | - Vijay Pandey
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China
| | - Ijaz Gul
- School of Communication Engineering, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China.
| | - Peiwu Qin
- School of Communication Engineering, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong Province, China.
| |
Collapse
|
2
|
Mahmoud R, Kalivarathan J, Castillo AJ, Wang S, Fuglestad B, Kanak MA, Dhakal S. Aptabinding of tumor necrosis factor-α (TNFα) inhibits its proinflammatory effects and alleviates islet inflammation. Biotechnol J 2024; 19:e2300374. [PMID: 37772688 DOI: 10.1002/biot.202300374] [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: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 09/30/2023]
Abstract
Pancreatic islet cell transplantation (ICT) has emerged as an effective therapy for diabetic patients lacking endogenous insulin production. However, the islet graft function is compromised by a nonspecific inflammatory and thrombotic reaction known as the instant blood-meditated inflammatory reaction (IBMIR). Here, we report the characterization of four single-stranded DNA aptamers that bind specifically to TNFα - a pivotal cytokine that causes proinflammatory signaling during the IBMIR process - using single molecule binding analysis and functional assays as a means to assess the aptamers' ability to block TNFα activity and inhibiting the downstream proinflammatory gene expression in the islets. Our single-molecule fluorescence analyses of mono- and multivalent aptamers showed that they were able to bind effectively to TNFα with monoApt2 exhibiting the strongest binding (Kd ∼ 0.02 ± 0.01 nM), which is ∼3 orders of magnitude smaller than the Kd of the other aptamers. Furthermore, the in vitro cell viability analysis demonstrated an optimal and safe dosage of 100 μM for monoApt2 compared to 50 μM for monoApt1 and significant protection from proinflammatory cytokine-mediated cell death. More interestingly, monoApt2 reversed the upregulation of IBMIR mediating genes induced by TNFα in the human islets, and this was comparable to established TNFα antagonists. Both monoaptamers showed high specificity and selectivity for TNFα. Collectively, these findings suggest the potential use of aptamers as anti-inflammatory and localized immune-modulating agents for cellular transplant therapy.
Collapse
Affiliation(s)
- Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jagan Kalivarathan
- Department of Surgery, Virginia Commonwealth University - School of Medicine, Virginia, USA
- Islet Cell Lab, Hume-Lee Transplant Center, VCU Health System, Richmond, Virginia, USA
| | - Abdul J Castillo
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Sasha Wang
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Brian Fuglestad
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Mazhar A Kanak
- Department of Surgery, Virginia Commonwealth University - School of Medicine, Virginia, USA
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, USA
| |
Collapse
|
3
|
Sabbih GO, Wijesinghe KM, Algama C, Dhakal S, Danquah MK. Computational generation and characterization of IsdA-binding aptamers with single-molecule FRET analysis. Biotechnol J 2023; 18:e2300076. [PMID: 37593983 DOI: 10.1002/biot.202300076] [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: 02/16/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Staphylococcus aureus is a major foodborne bacterial pathogen. Early detection of S. aureus is crucial to prevent infections and ensure food quality. The iron-regulated surface determinant protein A (IsdA) of S. aureus is a unique surface protein necessary for sourcing vital iron from host cells for the survival and colonization of the bacteria. The function, structure, and location of the IsdA protein make it an important protein for biosensing applications relating to the pathogen. Here, we report an in-silico approach to develop and validate high-affinity binding aptamers for the IsdA protein detection using custom-designed in-silico tools and single-molecule Fluorescence Resonance Energy Transfer (smFRET) measurements. We utilized in-silico oligonucleotide screening methods and metadynamics-based methods to generate 10 aptamer candidates and characterized them based on the Dissociation Free Energy (DFE) of the IsdA-aptamer complexes. Three of the aptamer candidates were shortlisted for smFRET experimental analysis of binding properties. Limits of detection in the low picomolar range were observed for the aptamers, and the results correlated well with the DFE calculations, indicating the potential of the in-silico approach to support aptamer discovery. This study showcases a computational SELEX method in combination with single-molecule binding studies deciphering effective aptamers against S. aureus IsdA, protein. The established approach demonstrates the ability to expedite aptamer discovery that has the potential to cut costs and predict binding efficacy. The application can be extended to designing aptamers for various protein targets, enhancing molecular recognition, and facilitating the development of high-affinity aptamers for multiple uses.
Collapse
Affiliation(s)
| | | | - Chamika Algama
- Virginia Commonwealth University, Richmond, Virginia, USA
| | - Soma Dhakal
- Virginia Commonwealth University, Richmond, Virginia, USA
| | - Michael K Danquah
- University of Tennessee, Chattanooga, Tennessee, USA
- University of Tennessee, Knoxville, Tennessee, USA
| |
Collapse
|
4
|
Keriel NA, Delezoide C, Chauvin D, Korri-Youssoufi H, Lai ND, Ledoux-Rak I, Nguyen CT. Optofluidic Sensor Based on Polymer Optical Microresonators for the Specific, Sensitive and Fast Detection of Chemical and Biochemical Species. SENSORS (BASEL, SWITZERLAND) 2023; 23:7373. [PMID: 37687829 PMCID: PMC10490054 DOI: 10.3390/s23177373] [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: 07/20/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023]
Abstract
The accurate, rapid, and specific detection of DNA strands in solution is becoming increasingly important, especially in biomedical applications such as the trace detection of COVID-19 or cancer diagnosis. In this work we present the design, elaboration and characterization of an optofluidic sensor based on a polymer-based microresonator which shows a quick response time, a low detection limit and good sensitivity. The device is composed of a micro-racetrack waveguide vertically coupled to a bus waveguide and embedded within a microfluidic circuit. The spectral response of the microresonator, in air or immersed in deionised water, shows quality factors up to 72,900 and contrasts up to 0.9. The concentration of DNA strands in water is related to the spectral shift of the microresonator transmission function, as measured at the inflection points of resonance peaks in order to optimize the signal-over-noise ratio. After functionalization by a DNA probe strand on the surface of the microresonator, a specific and real time measurement of the complementary DNA strands in the solution is realized. Additionally, we have inferred the dissociation constant value of the binding equilibrium of the two complementary DNA strands and evidenced a sensitivity of 16.0 pm/µM and a detection limit of 121 nM.
Collapse
Affiliation(s)
- Nolwenn-Amandine Keriel
- Laboratoire Lumière, Matière et Interfaces (LuMIn), Ecole Normale Superieure Paris Saclay, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 9024, CentraleSupelec, Institut d’Alembert, Université Paris Saclay, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France; (N.-A.K.); (N.D.L.); (C.-T.N.)
| | - Camille Delezoide
- Laboratoire Lumière, Matière et Interfaces (LuMIn), Ecole Normale Superieure Paris Saclay, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 9024, CentraleSupelec, Institut d’Alembert, Université Paris Saclay, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France; (N.-A.K.); (N.D.L.); (C.-T.N.)
| | - David Chauvin
- Laboratoire Lumière, Matière et Interfaces (LuMIn), Ecole Normale Superieure Paris Saclay, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 9024, CentraleSupelec, Institut d’Alembert, Université Paris Saclay, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France; (N.-A.K.); (N.D.L.); (C.-T.N.)
| | - Hafsa Korri-Youssoufi
- Institut de Chimie Moléculaire et des Matériaux d’Orsay (ICMMO), Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8182, Université Paris Saclay, 17 Avenue des Sciences, 91400 Orsay, France;
| | - Ngoc Diep Lai
- Laboratoire Lumière, Matière et Interfaces (LuMIn), Ecole Normale Superieure Paris Saclay, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 9024, CentraleSupelec, Institut d’Alembert, Université Paris Saclay, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France; (N.-A.K.); (N.D.L.); (C.-T.N.)
| | - Isabelle Ledoux-Rak
- Laboratoire Lumière, Matière et Interfaces (LuMIn), Ecole Normale Superieure Paris Saclay, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 9024, CentraleSupelec, Institut d’Alembert, Université Paris Saclay, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France; (N.-A.K.); (N.D.L.); (C.-T.N.)
| | - Chi-Thanh Nguyen
- Laboratoire Lumière, Matière et Interfaces (LuMIn), Ecole Normale Superieure Paris Saclay, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 9024, CentraleSupelec, Institut d’Alembert, Université Paris Saclay, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France; (N.-A.K.); (N.D.L.); (C.-T.N.)
| |
Collapse
|
5
|
Wijesinghe KM, Sabbih G, Algama CH, Syed R, Danquah MK, Dhakal S. FRET-Based Single-Molecule Detection of Pathogen Protein IsdA Using Computationally Selected Aptamers. Anal Chem 2023. [PMID: 37327207 DOI: 10.1021/acs.analchem.3c00717] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Iron-regulated surface determinant protein A (IsdA) is a key surface protein found in the foodborne bacteria─Staphylococcus aureus (S. aureus)─which is known to be critical for bacterial survival and colonization. S. aureus is pathogenic and has been linked to foodborne diseases; thus, early detection is critical to prevent diseases caused by this bacterium. Despite IsdA being a specific marker for S. aureus and several detection methods have been developed for sensitive detection of this bacteria such as cell culture, nucleic acids amplification, and other colorimetric and electrochemical methods, the detection of S. aureus through IsdA is underdeveloped. Here, by combining computational generation of target-guided aptamers and fluorescence resonance energy transfer (FRET)-based single-molecule analysis, we presented a widely applicable and robust detection method for IsdA. Three different RNA aptamers specific to the IsdA protein were identified and their ability to switch a FRET construct to a high-FRET state in the presence of protein was verified. The presented approach demonstrated the detection of IsdA down to picomolar levels (×10-12 M, equivalent to ∼1.1 femtomoles IsdA) with a dynamic range extending to ∼40 nM. The FRET-based single-molecule technique that we reported here is capable of detecting the foodborne pathogen protein IsdA with high sensitivity and specificity and has a broader application in the food industry and aptamer-based sensing field by enabling quantitative detection of a wide range of pathogen proteins.
Collapse
Affiliation(s)
- Kalani M Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Godfred Sabbih
- Department of Chemical Engineering, University of Tennessee, Chattanooga, Tennessee 37403, United States
| | - Chamika Harshani Algama
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Rida Syed
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Michael K Danquah
- Department of Chemical Engineering, University of Tennessee, Chattanooga, Tennessee 37403, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| |
Collapse
|
6
|
Han X, Du J, Shi D, Li L, Li D, Zhang K, Lin S, Zhu J, Huang Z, Zhou Y, Fang Z. Improving Reporter Gene Assay Methodology for Evaluating the Ability of Compounds to Restore P53 Activity. Int J Mol Sci 2022; 23:ijms232213867. [PMID: 36430341 PMCID: PMC9694221 DOI: 10.3390/ijms232213867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Tumor suppressor protein P53 induces cycle arrest and apoptosis by mediating the transcriptional expression of its target genes. Mutations causing conformational abnormalities and post-translational modifications that promote degradation are the main reasons for the loss of P53 function in tumor cells. Reporter gene assays that can scientifically reflect the biological function can help discover the mechanism and therapeutic strategies that restore P53 function. In the reporter gene system of this work, tetracycline-inducible expression of wild-type P53 was used to provide a fully activated state as a 100% activity reference for the objective measurement of biological function. It was confirmed by RT-qPCR, cell viability assay, immunofluorescence, and Western blot analysis that the above-mentioned reporter gene system could correctly reflect the differences in biological activity between the wild-type and mutants. After that, the system was tentatively used for related mechanism research and compound activity evaluation. Through the tetracycline-induced co-expression of wild-type P53 and mutant P53 in exact proportion, it was observed that the response modes of typical transcriptional response elements (TREs) to dominant negative P53 mutation effect were not exactly the same. Compared to the relative multiple-to-solvent control, the activity percentage relative to the 100% activity reference of wild-type P53 can better reflect the actual influence of the so-called P53 mutant reactivator. Similarly, relative to the 100% activity reference, it can objectively reflect the biological effects caused by the inhibitor of P53 negative factors, such as MDM2. In conclusion, this study provides a 100% activity reference and a reliable calculation model for relevant basic research and drug development.
Collapse
Affiliation(s)
- Xinle Han
- Biomedical Research Institute, Shenzhen Peking University—The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
- Department of Pathology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Jun Du
- Department of Hematology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Dandan Shi
- Shenzhen Chipscreen Biosciences Co., Ltd., Shenzhen Hi-Tech Industrial Park, Shenzhen 518057, China
| | - Lingjie Li
- Shenzhen Chipscreen Biosciences Co., Ltd., Shenzhen Hi-Tech Industrial Park, Shenzhen 518057, China
| | - Dandan Li
- Shenzhen Chipscreen Biosciences Co., Ltd., Shenzhen Hi-Tech Industrial Park, Shenzhen 518057, China
| | - Kun Zhang
- Shenzhen Chipscreen Biosciences Co., Ltd., Shenzhen Hi-Tech Industrial Park, Shenzhen 518057, China
| | - Suwen Lin
- Biomedical Research Institute, Shenzhen Peking University—The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
| | - Jingzhong Zhu
- Shenzhen Chipscreen Biosciences Co., Ltd., Shenzhen Hi-Tech Industrial Park, Shenzhen 518057, China
| | - Zoufang Huang
- Ganzhou Key Laboratory of Hematology, Department of Hematology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - You Zhou
- Shenzhen Chipscreen Biosciences Co., Ltd., Shenzhen Hi-Tech Industrial Park, Shenzhen 518057, China
- Correspondence: (Y.Z.); (Z.F.)
| | - Zhengyu Fang
- Biomedical Research Institute, Shenzhen Peking University—The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China
- Department of Pathology, Peking University Shenzhen Hospital, Shenzhen 518036, China
- Correspondence: (Y.Z.); (Z.F.)
| |
Collapse
|
7
|
Khamari L, Mukherjee S. Deciphering the Nanoconfinement Effect on the Folding Pathway of c-MYC Promoter-Based Intercalated-Motif DNA by Single-Molecule Förster Resonance Energy Transfer. J Phys Chem Lett 2022; 13:8169-8176. [PMID: 36005552 DOI: 10.1021/acs.jpclett.2c01893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Intercalated-motif (i-motif) DNA formed by cytosine (C)-rich sequences has been considered a novel target in anticancer research. Interestingly, this type of noncanonical DNA structure is highly dynamic and can display several conformational polymorphisms based on the immediate surrounding environment. However, studies regarding the folding pathway of i-motifs having disease-specific sequences under a confined environment at physiological pH are relatively scarce. This thereby warrants more explorations that will decipher their structural and functional properties inside constrained media. Herein, using the single-molecule Förster Resonance Energy Transfer (smFRET) studies, for the first time, we have illustrated the conformational dynamics of c-MYC promoter-based i-motif structures at physiological pH inside microemulsions of different dimensions. We concluded that the folding of such motifs under confined space is not a direct transition between the random coil and i-motif conformations; rather it occurs through a partially folded intermediate, depending on the confined dimension.
Collapse
Affiliation(s)
- Laxmikanta Khamari
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal 462 066, Madhya Pradesh, India
| |
Collapse
|
8
|
Ghimire ML, Gibbs DR, Mahmoud R, Dhakal S, Reiner JE. Nanopore Analysis as a Tool for Studying Rapid Holliday Junction Dynamics and Analyte Binding. Anal Chem 2022; 94:10027-10034. [PMID: 35786863 DOI: 10.1021/acs.analchem.2c00342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Holliday junctions (HJs) are an important class of nucleic acid structure utilized in DNA break repair processes. As such, these structures have great importance as therapeutic targets and for understanding the onset and development of various diseases. Single-molecule fluorescence resonance energy transfer (smFRET) has been used to study HJ structure-fluctuation kinetics, but given the rapid time scales associated with these kinetics (approximately sub-milliseconds) and the limited bandwidth of smFRET, these studies typically require one to slow down the structure fluctuations using divalent ions (e.g., Mg2+). This modification limits the ability to understand and model the underlying kinetics associated with HJ fluctuations. We address this here by utilizing nanopore sensing in a gating configuration to monitor DNA structure fluctuations without divalent ions. A nanopore analysis shows that HJ fluctuations occur on the order of 0.1-10 ms and that the HJ remains locked in a single conformation with short-lived transitions to a second conformation. It is not clear what role the nanopore plays in affecting these kinetics, but the time scales observed indicate that HJs are capable of undergoing rapid transitions that are not detectable with lower bandwidth measurement techniques. In addition to monitoring rapid HJ fluctuations, we also report on the use of nanopore sensing to develop a highly selective sensor capable of clear and rapid detection of short oligo DNA strands that bind to various HJ targets.
Collapse
Affiliation(s)
- Madhav L Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Dalton R Gibbs
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| |
Collapse
|
9
|
Wijesinghe KM, Kanak MA, Harrell JC, Dhakal S. Single-Molecule Sensor for High-Confidence Detection of miRNA. ACS Sens 2022; 7:1086-1094. [PMID: 35312280 PMCID: PMC9112324 DOI: 10.1021/acssensors.1c02748] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) play a crucial role in regulating gene expression and have been linked to many diseases. Therefore, sensitive and accurate detection of disease-linked miRNAs is vital to the emerging revolution in early diagnosis of diseases. While the detection of miRNAs is a challenge due to their intrinsic properties such as small size, high sequence similarity among miRNAs and low abundance in biological fluids, the majority of miRNA-detection strategies involve either target/signal amplification or involve complex sensing designs. In this study, we have developed and tested a DNA-based fluorescence resonance energy transfer (FRET) sensor that enables ultrasensitive detection of a miRNA biomarker (miRNA-342-3p) expressed by triple-negative breast cancer (TNBC) cells. The sensor shows a relatively low FRET state in the absence of a target but it undergoes continuous FRET transitions between low- and high-FRET states in the presence of the target. The sensor is highly specific, has a detection limit down to low femtomolar (fM) without having to amplify the target, and has a large dynamic range (3 orders of magnitude) extending to 300 000 fM. Using this strategy, we demonstrated that the sensor allows detection of miRNA-342-3p in the miRNA-extracts from cancer cell lines and TNBC patient-derived xenografts. Given the simple-to-design hybridization-based detection, the sensing platform developed here can be used to detect a wide range of miRNAs enabling early diagnosis and screening of other genetic disorders.
Collapse
Affiliation(s)
- Kalani M. Wijesinghe
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Mazhar A. Kanak
- Division of Transplant Surgery, Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, United States
| | - J. Chuck Harrell
- Department of Pathology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| |
Collapse
|
10
|
Plasmon-modulated fluorescence nanoprobes for enzyme-free DNA detection via target signal enhancement and off-target quenching. Biosens Bioelectron 2022; 210:114288. [DOI: 10.1016/j.bios.2022.114288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022]
|
11
|
Ceresa L, Chavez J, Bus MM, Budowle B, Kitchner E, Kimball J, Gryczynski I, Gryczynski Z. Förster Resonance Energy Transfer-Enhanced Detection of Minute Amounts of DNA. Anal Chem 2022; 94:5062-5068. [PMID: 35286067 DOI: 10.1021/acs.analchem.1c05275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article presents a novel approach to increase the detection sensitivity of trace amounts of DNA in a sample by employing Förster resonance energy transfer (FRET) between intercalating dyes. Two intercalators that present efficient FRET were used to enhance sensitivity and improve specificity in detecting minute amounts of DNA. Comparison of steady-state acceptor emission spectra with and without the donor allows for simple and specific detection of DNA (acceptor bound to DNA) down to 100 pg/μL. When utilizing as an acceptor a dye with a significantly longer lifetime (e.g., ethidium bromide bound to DNA), multipulse pumping and time-gated detection enable imaging/visualization of picograms of DNA present in a microliter of an unprocessed sample or DNA collected on a swab or other substrate materials.
Collapse
Affiliation(s)
- Luca Ceresa
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Jose Chavez
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Magdalena M Bus
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United States.,Department of Microbiology, Immunology & Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United States
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United States.,Department of Microbiology, Immunology & Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, Texas 76107, United States
| | - Emma Kitchner
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Joseph Kimball
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Ignacy Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| | - Zygmunt Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas 76109, United States
| |
Collapse
|
12
|
Marquezin CA, Lamy MT, de Souza ES. Molecular collisions or resonance energy transfer in lipid vesicles? A methodology to tackle this question. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Wu LZ, Ye Y, Wang ZX, Ma D, Li L, Xi GH, Bao BQ, Weng LX. Sensitive Detection of Single-Nucleotide Polymorphisms by Solid Nanopores Integrated With DNA Probed Nanoparticles. Front Bioeng Biotechnol 2021; 9:690747. [PMID: 34277589 PMCID: PMC8279778 DOI: 10.3389/fbioe.2021.690747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 12/01/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the abundant forms of genetic variations, which are closely associated with serious genetic and inherited diseases, even cancers. Here, a novel SNP detection assay has been developed for single-nucleotide discrimination by nanopore sensing platform with DNA probed Au nanoparticles as transport carriers. The SNP of p53 gene mutation in gastric cancer has been successfully detected in the femtomolar concentration by nanopore sensing. The robust biosensing strategy offers a way for solid nanopore sensors integrated with varied nanoparticles to achieve single-nucleotide distinction with high sensitivity and spatial resolution, which promises tremendous potential applications of nanopore sensing for early diagnosis and disease prevention in the near future.
Collapse
Affiliation(s)
- Ling Zhi Wu
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China.,College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Yuan Ye
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Zhi Xuan Wang
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Die Ma
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Li Li
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Guo Hao Xi
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Bi Qing Bao
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Li Xing Weng
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| |
Collapse
|