1
|
Zhang W, Li W, Song Y, Xu Q, Xu H. Bacterial detection based on Förster resonance energy transfer. Biosens Bioelectron 2024; 255:116244. [PMID: 38547644 DOI: 10.1016/j.bios.2024.116244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/15/2024]
Abstract
The huge economic loss and threat to human health caused by bacterial infection have attracted the public's concern, and there is an urgent need to relieve and improve the tough problem. Therefore, it is significant to establish a facile, rapid, and sensitive method for bacterial detection considering the shortcomings of existing methods. Förster resonance energy transfer (FRET)-based sensors have exhibited immense potential and applicability for bacterial detection given their high signal-to-noise ratio and high sensitivity. This review focuses on the development of FRET-based fluorescence assays for bacterial detection. We summarize the principle of FRET-based assays, discuss the commonly used recognition molecules and further introduce three frequent construction strategies. Based on the strategies and materials, relevant applications are presented. Moreover, some restrictions of FRET fluorescence sensors and development prospects are discussed. Suitable donor-acceptor pairs and stable recognition molecules are the essential conditions for sensors to play their roles, and there is still some room for development. Besides, applying FRET fluorescence sensors to point-of-care detection is still difficult. Future developments could focus on near-infrared fluorescent dyes and simultaneous detection of multiple analytes.
Collapse
Affiliation(s)
- Wanqing Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR China
| | - Weiqiang Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR China
| | - Yang Song
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR China
| | - Qian Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang, 330047, PR China.
| |
Collapse
|
2
|
Chen H, Tian P, Guo J, Sun M, Zhu W, Li Z, Liu Z. Synergistic synthesis of gold nanoflowers as upconversion near-infrared nanoprobe energy acceptor and recognition unit for improved hydrogen sulfide sensing. Talanta 2024; 273:125908. [PMID: 38503119 DOI: 10.1016/j.talanta.2024.125908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 03/03/2024] [Accepted: 03/09/2024] [Indexed: 03/21/2024]
Abstract
A highly sensitive and selective upconversion near-infrared (NIR) fluorescence and colorimetric dual readout hydrogen sulfide (H2S) nanoprobe was constructed based on the excellent NIR fluorescence emission performance of upconversion nanomaterials (UCNPs), the specific recognition effect of synergistically synthesized gold nanoflowers (trypsin-stabled AuNFs (Try-AuNFs)) and the effective NIR fluorescence quenching capability. In this assay, the sensing strategy included three processes. First of all, the synthesized UCNPs can emit 803 nm NIR fluorescence when they were excited by 980 nm excitation light. Secondly, as a result of the principle of fluorescence resonance energy transfer (FRET), Try-AuNFs can effectively quench the NIR fluorescence of UCNPs at 803 nm, which can effectively improve the signal-to-background ratio of nanoprobes, thereby improving the sensitivity of the probes. Thirdly, in the presence of H2S, the Try protective layer on the surface of Try-AuNFs was specifically penetrated, which will subsequently cleave Try-AuNFs via the strong S-Au bond. As such, the NIR fluorescence of UCNPs will be restored, achieving high selectivity and sensitivity detection of H2S. Under optimized conditions, the linear response range of H2S was 0.1-300 μM, and the detection limit was 53 nM. It is worth noting that the Try on the surface of Try-AuNFs via the synergistic effect can increase the steric hindrance of the probe, and this can effectively prevent the interaction between the probe with biothiols (cysteine (Cys), homocysteine (Hcy)) and other natural amino acids (non-thiol-containing) with resultant in the high selectivity regarding the detection of H2S in human serum, which is unlikely to be achieved by AuNFs synthesized by the gold seed method (Se-AuNFs). This work not only provided a new type of UCNPs fluorescence quencher and recognition unit, but also exemplified that the use of the physical properties (steric hindrance) of protein ligands on the surface of nanoflowers can improve the specificity of the probe. This will provide new ideas for the design of other nanoprobes.
Collapse
Affiliation(s)
- Hongyu Chen
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China.
| | - Peipei Tian
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China
| | - Jiayi Guo
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China
| | - Manman Sun
- College of Physics and Telecommunication Engineering, Zhoukou Normal University, Zhoukou 466001, China.
| | - Wenping Zhu
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China
| | - Zhendong Li
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China
| | - Zengchen Liu
- Henan Key Laboratory of Rare Earth Functional Materials, International Joint Research Laboratory for Biomedical Nanomaterials of Henan, Zhoukou Normal University, Zhoukou 466001, China.
| |
Collapse
|
3
|
Chaghazardi M, Kashanian S, Nazari M, Omidfar K, Shariati-Rad M, Joseph Y, Rahimi P. Mercury (II) sensing using a simple turn-on fluorescent graphene oxide based aptasensor in serum and water samples. Spectrochim Acta A Mol Biomol Spectrosc 2024; 313:124057. [PMID: 38457872 DOI: 10.1016/j.saa.2024.124057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 03/10/2024]
Abstract
A simple, highly sensitive, and selective fluorometric aptasensing platform based on aptamer and graphene oxide (GO) is proposed for the determination of mercury (II) ion (Hg2+). In the designed assay, two aptamer probes, a carboxy-fluorescein (FAM) labeled aptamer (aptamer A) and its complementary (aptamer B) with partial complement containing several mismatches and GO as the quencher were used. In the absence of Hg2+, both A and B aptamers were adsorbed on the surface of GO by π-π-stacking, leading to fluorescence quenching of FAM due to fluorescence resonance energy transfer (FRET). Upon exposure to Hg2+, the A and B aptamer strands bind Hg2+ and form T-Hg2+-T complexes, leading to the formation of a stable double-stranded aptamer. The double-stranded aptamer is detached from the GO surface, resulting in the recovery of FAM fluorescence. The fluorescence intensity (FI) of the developed sensor was correlated with the Hg2+ concentration under optimized experimental conditions in two wide linear ranges, even in the presence of 10 divalent cations as interferences. The linear ranges were obtained from 200.0 to 900.0 fM and 5.0 to 33.0 pM, a limit of detection (LOD) of 106.0 fM, and a limit of quantification (LOQ) of 321.3 fM. The concentration of Hg2+ was determined in five real samples containing three water and two serum samples, using spiking and standard addition methods and the results were compared with the spiked amounts and atomic absorption (AAS) as standard method respectively, with acceptable recoveries. Furthermore, in the standard addition method, to overcome the effects of matrix influence of real samples in quantitative predictions, the excitation-emission matrix (EEM) data for samples was simultaneously analyzed by multivariate curve resolution with alternating least squares (MCR-ALS) as a second-order standard addition method (SOSAM).
Collapse
Affiliation(s)
- Mosayeb Chaghazardi
- Faculty of Chemistry, Razi University, Kermanshah, Iran; Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Soheila Kashanian
- Faculty of Chemistry, Sensor and Biosensor Research Center (SBRC) & Nanoscience and Nanotechnology Research Center (NNRC), Razi University, Kermanshah, Iran; Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah, Iran.
| | - Maryam Nazari
- Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran; Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Shariati-Rad
- Department of Analytical Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran.
| | - Yvonne Joseph
- Institute of Nanoscale and Biobased Materials, Faculty of Materials Science and Materials Technology, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany; Water Research Center, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany
| | - Parvaneh Rahimi
- Institute of Nanoscale and Biobased Materials, Faculty of Materials Science and Materials Technology, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany; Water Research Center, Technische Universität Bergakademie Freiberg, 09599 Freiberg, Germany
| |
Collapse
|
4
|
Chen J, Zhang Y, Wang X, Li F, Wu S, Wang W, Zhou N. A FRET based ultrasensitive fluorescent aptasensor for 6'-sialyllactose detection. Anal Biochem 2024; 688:115462. [PMID: 38246433 DOI: 10.1016/j.ab.2024.115462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/01/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
As a kind of human milk oligosaccharide, 6'-sialyllactose (6'-SL) plays an important role in promoting infant brain development and improving infant immunity. The content of 6'-SL in infant formula milk powder is thus one of the important nutritional indexes. Since the lacking of efficient and rapid detection methods for 6'-SL, it is of great significance to develop specific recognition elements and establish fast and sensitive detection methods for 6'-SL. Herein, using 6'-SL specific aptamer as the recognition element, catalytic hairpin assembly as the signal amplification technology and quantum dots as the signal label, a fluorescence biosensor based on fluorescence resonance energy transfer (FRET) was constructed for ultra-sensitive detection of 6'-SL. The detection limit of this FRET-based fluorescent biosensor is 0.3 nM, and it has some outstanding characteristics such as high signal-to-noise ratio, low time-consuming, simplicity and high efficiency in the actual sample detection. Therefore, it has broad application prospect in 6'-SL detection.
Collapse
Affiliation(s)
- Jinri Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China; Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, China; State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuting Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoli Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Fuhou Li
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, China
| | - Shaojie Wu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, China
| | - Weixia Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou, 222005, China
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
5
|
Roccatano D. A molecular dynamics simulation study of glycine/serine octapeptides labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene fluorophore. J Chem Phys 2024; 160:145101. [PMID: 38587229 DOI: 10.1063/5.0190073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
The compound 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) is a versatile fluorophore widely used in Förster resonance energy transfer (FRET) spectroscopy studies due to its remarkable sensitivity, enabling precise donor-acceptor distance measurements, even for short peptides. Integrating time-resolved and FRET spectroscopies with molecular dynamics simulations provides a robust approach to unravel the structure and dynamics of biopolymers in a solution. This study investigates the structural behavior of three octapeptide variants: Trp-(Gly-Ser)3-Dbo, Trp-(GlyGly)3-Dbo, and Trp-(SerSer)3-Dbo, where Dbo represents the DBO-containing modified aspartic acid, using molecular dynamics simulations. Glycine- and serine-rich amino acid fragments, common in flexible protein regions, play essential roles in functional properties. Results show excellent agreement between end-to-end distances, orientational factors from simulations, and the available experimental and theoretical data, validating the reliability of the GROMOS force field model. The end-to-end distribution, modeled using three Gaussian distributions, reveals a complex shape, confirmed by cluster analysis highlighting a limited number of significant conformations dominating the peptide landscape. All peptides predominantly adopt a disordered state in the solvent, yet exhibit a compact shape, aligning with the model of disordered polypeptide chains in poor solvents. Conformations show marginal dependence on chain composition, with Ser-only chains exhibiting slightly more elongation. This study enhances our understanding of peptide behavior, providing valuable insights into their structural dynamics in solution.
Collapse
Affiliation(s)
- Danilo Roccatano
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln LN6 7TS, United Kingdom
| |
Collapse
|
6
|
Liu FT, Wang YP, Jiang PF, Zhao BX. A FRET-based ratiometric fluorescent probe for sensing bisulfite/sulfite and viscosity and its applications in food, water samples and test strips. Food Chem 2024; 436:137755. [PMID: 37862981 DOI: 10.1016/j.foodchem.2023.137755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/28/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023]
Abstract
A FRET-based ratiometric dual-response fluorescent probe, CQI, constructed by combining quinolinium-indole as the acceptor and coumarin as the donor, was developed for sensing HSO3-/SO32- and viscosity. After the interaction of probe CQI with the analyte, we achieved a green channel for the response to HSO3-/SO32- and an orange channel for the response to viscosity. We comprehensively evaluated the ability of CQI to detect SO2 derivatives and viscosity using fluorescence spectroscopy. Probe CQI exhibited a large Stokes shift (196 nm), a high energy transfer efficiency (99.6 %) and a wide detection range (0-250 μM). The fluorescence intensity of the probe increased up to 14-fold with increasing viscosity, and CQI could detect the viscosity of food thickeners. More importantly, probe CQI could not only successfully monitor SO2 derivatives in various food and water samples, but also be prepared as bisulfite test strips.
Collapse
Affiliation(s)
- Feng-Ting Liu
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Yan-Pu Wang
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Peng-Fei Jiang
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Bao-Xiang Zhao
- Institute of Organic Chemistry, School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China.
| |
Collapse
|
7
|
Rong Y, Hassan MM, Wu J, Chen S, Yang W, Li Y, Zhu J, Huang J, Chen Q. Enhanced detection of acrylamide using a versatile solid-state upconversion sensor through spectral and visual analysis. J Hazard Mater 2024; 466:133369. [PMID: 38278076 DOI: 10.1016/j.jhazmat.2023.133369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/14/2023] [Accepted: 12/23/2023] [Indexed: 01/28/2024]
Abstract
Acrylamide (AM) generally forms in high-temperature processes and has been classified as a potential carcinogen. In this study, we put forward a maneuverable solid-state luminescence sensor using polydimethylsiloxane (PDMS) as the matrix coupled with upconversion nanoparticles as the indicator. The core-shell upconversion nanoparticles emitting cyan light were uniformly encapsulated in PDMS. Then it was further modified with complementary DNA of AM aptamer. The nanocrystalline fluorescein isothiocyanate isomer (FITC), coupled with AM aptamer, was attached to the surface of PDMS. FITC effectively quenched the upconversion luminescence through fluorescence resonance energy transfer (FRET). The introduction of AM resulted in preferentially bound to aptamer caused the separation of the quencher and the donor, and led to luminescence recovery. The developed sensor was applied for both spectral and visual monitoring, demonstrating a detection limit (LOD) of 1.00 nM and 1.07 nM, respectively. Importantly, in the actual foodstuffs detection, there is no obvious difference between the results of this study and the standard method, which indicates the developed method has good accuracy. Therefore, this solid-state sensor has the potential for on-site detection using a smartphone device and an Android application.
Collapse
Affiliation(s)
- Yawen Rong
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, 310023, PR China
| | - Md Mehedi Hassan
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, PR China
| | - Jizhong Wu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Shuo Chen
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, 310023, PR China
| | - Wancheng Yang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, 310023, PR China
| | - Yunhao Li
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, 310023, PR China
| | - Jiaji Zhu
- School of Electrical Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Jun Huang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, 310023, PR China.
| | - Quansheng Chen
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, PR China; School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China.
| |
Collapse
|
8
|
Tseng WB, Wu MJ, Lu CY, Krishna Kumar AS, Tseng WL. Aptamer-based flares hybridized with single-stranded DNA-conjugated MoS 2 nanosheets for ratiometric fluorescence sensing and imaging of potassium ions and adenosine triphosphate in human fluids and living cells. Spectrochim Acta A Mol Biomol Spectrosc 2024; 309:123781. [PMID: 38176190 DOI: 10.1016/j.saa.2023.123781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/01/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024]
Abstract
Addressing the limitations observed in previous studies, where the quantitative range of nanoprobes for detecting K+ and adenosine triphosphate (ATP) did not cover concentrations found within living cells, the present study aimed to develop ratiometric nanoprobes that can accurately sense changes in K+ and ATP levels in living cells and quantify them in human fluids. The proposed nanoprobes consisted of recognition flares modified with 6-carboxyfluorescein (FAM) and 5-carboxytetramethylrhodamine (TAMRA), along with thiolate single-stranded DNA (ssDNA) and molybdenum disulfide nanosheets (MoS2 NSs). The thiolate ssDNA acts as a linker between the flares and the MoS2 NSs, directly forming a functional nanostructure at room temperature. The direct conjugation of labeled flares to the MoS2 NSs simplifies the fabrication process. In the absence of K+ and ATP, the hybridization of flares and thiolate ssDNA caused FAM to move away from TAMRA, suppressing the fluorescence resonance energy transfer (FRET) process. However, upon the introduction of K+ and ATP, the flares undergo a structural transformation via the formation of G-quadruplex formation and the generation of hairpin-shaped structures, respectively. This structural change leads to the release of the flares from the ssDNA-conjugated nanosheet surface. The release of the flares brings FAM and TAMRA into close proximity, allowing FRET to occur, leading to FRET and static quenching. By monitoring the ratio between the fluorescence intensities of FAM and TAMRA, the concentration of K+ (5-100 mM) and ATP (0.3-5 mM) can be accurately determined by the proposed nanoprobes. The advantages of these nanoprobes lie in their ability to provide ratiometric measurements, which enhance the accuracy and reliability of the quantification process. The proposed nanoprobes offer potential applications as ratiometric imaging probes for monitoring K+ and ATP-related reactions in living cells, providing valuable insights into cellular processes. Additionally, they can be employed for determining the levels of K+ and ATP in human fluids, offering potential diagnostic applications in various clinical settings.
Collapse
Affiliation(s)
- Wei-Bin Tseng
- Department of Chemistry and Center for Nanoscience & Nanotechnology, National Sun Yat-sen University, No. 70 Lienhai Rd., Kaohsiung 80424, Taiwan; Department of Environmental Engineering, Da-Yeh University, No. 168, University Rd., Dacun, Changhua 515006, Taiwan.
| | - Man-Jyun Wu
- Department of Chemistry and Center for Nanoscience & Nanotechnology, National Sun Yat-sen University, No. 70 Lienhai Rd., Kaohsiung 80424, Taiwan
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, No. 100, Shiquan First Road, Sanmin District, Kaohsiung 80708, Taiwan
| | - A Santhana Krishna Kumar
- Faculty of Geology, Geophysics and Environmental Protection, AGH University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow, Poland
| | - Wei-Lung Tseng
- Department of Chemistry and Center for Nanoscience & Nanotechnology, National Sun Yat-sen University, No. 70 Lienhai Rd., Kaohsiung 80424, Taiwan; School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, No. 100, Shiquan 1st Rd., 80708 Kaohsiung, Taiwan.
| |
Collapse
|
9
|
Zheng Y, Zhai SM, Xiao MM, Dong PZ, Xu JR, Zhao BX. A novel ratiometric fluorescence probe based on the FRET-ICT mechanism for detecting fluoride ions and viscosity. Spectrochim Acta A Mol Biomol Spectrosc 2024; 309:123822. [PMID: 38176193 DOI: 10.1016/j.saa.2023.123822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024]
Abstract
Fluoride ion is not only important for dental health, but also a contributing factor in a variety of diseases. At the same time, fluoride ions and cell viscosity are both important to the physiological environment of mitochondria. We developed a dual-response ratiometric fluorescent probe BDF based on Förster resonance energy transfer (FRET) and intramolecular charge transfer (ICT) mechanism for the detection of F- and viscosity. BDF has an outstanding intramolecular energy transfer efficiency of 97.7% and shows excellent performance for fluorine ion detection. In addition, when the system viscosity increases, the fluorescence emission intensity of BDF is greatly heightened, indicating the possibility of viscosity detection. Finally, based on the fluorescence properties of BDF, we used the probe to detect F- in the toothpaste sample and image exogenous fluoride ions in HeLa cells.
Collapse
Affiliation(s)
- Yi Zheng
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Shu-Mei Zhai
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China.
| | - Meng-Min Xiao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Pei-Zhen Dong
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Jia-Rui Xu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China
| | - Bao-Xiang Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, PR China.
| |
Collapse
|
10
|
Chen J, Ho WKH, Yin B, Zhang Q, Li C, Yan J, Huang Y, Hao J, Yi C, Zhang Y, Wong SHD, Yang M. Magnetic-responsive upconversion luminescence resonance energy transfer (LRET) biosensor for ultrasensitive detection of SARS-CoV-2 spike protein. Biosens Bioelectron 2024; 248:115969. [PMID: 38154329 DOI: 10.1016/j.bios.2023.115969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/08/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Upconversion nanoparticles (UCNPs) are ideal donors for luminescence resonance energy transfer (LRET)-based biosensors due to their excellent upconversion luminescence properties. However, the relatively large size of antibodies and proteins limits the application of UCNPs-based LRET biosensors in protein detection because the large steric hindrance of proteins leads to low energy transfer efficiency between UCNPs and receptors. Herein, we developed a magnetic responsive UCNPs-based LRET biosensor to control the coupling distance between antibody-functionalized UCNPs (Ab-UCNPs) as donors and antibody-PEG linker-magnetic gold nanoparticles (Ab-PEG-MGNs) as acceptors for ultrasensitive and highly selective detection of SARS-CoV-2 spike proteins. Our results showed that this platform reversibly shortened the coupling distance between UCNPs and MGNs and enhanced the LRET signal with a 10-fold increase in the limit of detection (LOD) from 20.6 pg/mL without magnetic modulation to 2.1 pg/mL with magnetic modulation within 1 h. The finite-difference time-domain (FDTD) simulation with cyclic distance change confirmed the distance-dependent LRET efficiency under magnetic modulation, which supported the experimental results. Moreover, the applications of this magnetic-responsive UCNP-based LRET biosensor could be extended to other large-size biomolecule detection.
Collapse
Affiliation(s)
- Jiareng Chen
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China
| | - Willis Kwun Hei Ho
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China
| | - Bohan Yin
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China
| | - Qin Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China
| | - Chuanqi Li
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China
| | - Jiaxiang Yan
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China
| | - Yingying Huang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China
| | - Jianhua Hao
- Department of Applied Physics, The Hong Kong Polytechnic University, 999077, Hong Kong, China
| | - Changqing Yi
- Key Laboratory of Sensing Technology and Biomedical Instruments Guangdong, School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou, 510006, China
| | - Yu Zhang
- Department of Mechanical and Automotive Engineering, Royal Melbourne Institute of Technology, Melbourne, VIC, 3000, Australia
| | - Siu Hong Dexter Wong
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China.
| | - Mo Yang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, 999077, Hong Kong, China.
| |
Collapse
|
11
|
Zhao X, Xu Y, Chen Z, Tang C, Mi X. Encoding fluorescence intensity with tetrahedron DNA nanostructure based FRET effect for bio-detection. Biosens Bioelectron 2024; 248:115994. [PMID: 38181517 DOI: 10.1016/j.bios.2023.115994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/20/2023] [Accepted: 12/29/2023] [Indexed: 01/07/2024]
Abstract
Biocoding technology constructed by readable tags with distinct signatures is a brand-new bioanalysis method to realize multiplexed identification and bio-information decoding. In this study, a novel fluorescence intensity coding technology termed Tetra-FICT was reported based on tetrahedron DNA nanostructure (TDN) carrier and Főrster Resonance Energy Transfer (FRET) effect. By modulating numbers and distances of Cy3 and Cy5 at four vertexes of TDN, different fluorescence intensities of twenty-six samples were produced at ∼565.0 nm (FICy3) and ∼665.0 nm (FICy5) by detecting fluorescence spectra. By developing an error correction mechanism, eleven codes were established based on divided intensity ranges of the final FICy3 together with FICy5 (Final-FICy3&FICy5). These resulting codes were used to construct barcode probes, with three miRNA biomarkers (miRNA-210, miRNA-199a and miRNA-21) as cases for multiplexed bio-assay. The high specificity and sensitivity were also demonstrated for the detection of miRNA-210. Overall, the proposed Tetra-FICT enriched the toolbox of fluorescence coding, which could be applied to multiplexing biomarkers detection.
Collapse
Affiliation(s)
- Xiaoshuang Zhao
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; School of Physics and Optoelectronic Engineering, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Yi Xu
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China
| | - Ziting Chen
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Chengren Tang
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Xianqiang Mi
- National Key Laboratory of Materials for Integrated Circuits, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai, 200050, China; Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, 201210, China; School of Physics and Optoelectronic Engineering, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; University of Chinese Academy of Science, Beijing, 100049, China.
| |
Collapse
|
12
|
Peng F, Ai X, Sun J, Yang L, Gao B. Recent advances in FRET probes for mitochondrial imaging and sensing. Chem Commun (Camb) 2024; 60:2994-3007. [PMID: 38381520 DOI: 10.1039/d4cc00018h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Mitochondria, as essential organelles in cells, play a crucial role in cellular growth and apoptosis. Monitoring mitochondria is of great importance, as mitochondrial dysfunction is often considered a hallmark event of cell apoptosis. Traditional fluorescence probes used for mitochondrial imaging and sensing are mostly intensity-based and are susceptible to factors such as concentration, the probe environment, and fluorescence intensity. Probes based on fluorescence resonance energy transfer (FRET) can effectively overcome external interference and achieve high-contrast imaging of mitochondria as well as quantitative monitoring of mitochondrial microenvironments. This review focuses on recent advances in the application of FRET-based probes for mitochondrial structure imaging and microenvironment sensing.
Collapse
Affiliation(s)
- Fei Peng
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
| | - Xiangnan Ai
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
| | - Jing Sun
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
| | - Linshuai Yang
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
| | - Baoxiang Gao
- College of Chemistry and Materials Science, Hebei University, Baoding, 071002, China.
- Key Laboratory of Analytical Science and Technology of Hebei Province, Hebei University, Baoding 071002, Hebei, China
| |
Collapse
|
13
|
Montepietra D, Tesei G, Martins JM, Kunze MBA, Best RB, Lindorff-Larsen K. FRETpredict: a Python package for FRET efficiency predictions using rotamer libraries. Commun Biol 2024; 7:298. [PMID: 38461354 PMCID: PMC10925062 DOI: 10.1038/s42003-024-05910-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 02/12/2024] [Indexed: 03/11/2024] Open
Abstract
Förster resonance energy transfer (FRET) is a widely-used and versatile technique for the structural characterization of biomolecules. Here, we introduce FRETpredict, an easy-to-use Python software to predict FRET efficiencies from ensembles of protein conformations. FRETpredict uses a rotamer library approach to describe the FRET probes covalently bound to the protein. The software efficiently and flexibly operates on large conformational ensembles such as those generated by molecular dynamics simulations to facilitate the validation or refinement of molecular models and the interpretation of experimental data. We provide access to rotamer libraries for many commonly used dyes and linkers and describe a general methodology to generate new rotamer libraries for FRET probes. We demonstrate the performance and accuracy of the software for different types of systems: a rigid peptide (polyproline 11), an intrinsically disordered protein (ACTR), and three folded proteins (HiSiaP, SBD2, and MalE). FRETpredict is open source (GPLv3) and is available at github.com/KULL-Centre/FRETpredict and as a Python PyPI package at pypi.org/project/FRETpredict .
Collapse
Affiliation(s)
- Daniele Montepietra
- Department of Chemical, Life and Environmental Sustainability Sciences, University of Parma, Parma, 43125, Italy
- Istituto Nanoscienze - CNR-NANO, Center S3, via G. Campi 213/A, 41125, Modena, Italy
| | - Giulio Tesei
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - João M Martins
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Micha B A Kunze
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892-0520, USA.
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark.
| |
Collapse
|
14
|
Michelis S, Pompili C, Niedergang F, Fattaccioli J, Dumat B, Mallet JM. FRET-Sensing of Multivalent Protein Binding at the Interface of Biomimetic Microparticles Functionalized with Fluorescent Glycolipids. ACS Appl Mater Interfaces 2024; 16:9669-9679. [PMID: 38349191 DOI: 10.1021/acsami.3c15067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Cell adhesion is a central process in cellular communication and regulation. Adhesion sites are triggered by specific ligand-receptor interactions inducing the clustering of both partners at the contact point. Investigating cell adhesion using microscopy techniques requires targeted fluorescent particles with a signal sensitive to the clustering of receptors and ligands at the interface. Herein, we report on simple cell or bacterial mimics, based on liquid microparticles made of lipiodol functionalized with custom-designed fluorescent lipids. These lipids are targeted toward lectins or biotin membrane receptors, and the resulting particles can be specifically identified and internalized by cells, as demonstrated by their phagocytosis in primary murine bone marrow-derived macrophages. We also evidence the possibility to sense the binding of a multivalent lectin, concanavalin A, in solution by monitoring the energy transfer between two matching fluorescent lipids on the surface of the particles. We anticipate that these liquid particle-based sensors, which are able to report via Förster resonance energy transfer (FRET) on the movement of ligands on their interface upon protein binding, will provide a useful tool to study receptor binding and cooperation during adhesion processes such as phagocytosis.
Collapse
Affiliation(s)
- Sophie Michelis
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Chiara Pompili
- Université Paris Cité, Institut Cochin, INSERM, CNRS, 75014 Paris, France
| | | | - Jacques Fattaccioli
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL Université, Sorbonne Université, CNRS, 75005 Paris, France
- Institut Pierre-Gilles de Gennes pour la Microfluidique, 75005 Paris, France
| | - Blaise Dumat
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| |
Collapse
|
15
|
Johnson SC, Annamdevula NS, Leavesley SJ, Francis CM, Rich TC. Hyperspectral imaging and dynamic region of interest tracking approaches to quantify localized cAMP signals. Biochem Soc Trans 2024; 52:191-203. [PMID: 38334148 DOI: 10.1042/bst20230352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 02/10/2024]
Abstract
Cyclic adenosine monophosphate (cAMP) is a ubiquitous second messenger known to orchestrate a myriad of cellular functions over a wide range of timescales. In the last 20 years, a variety of single-cell sensors have been developed to measure second messenger signals including cAMP, Ca2+, and the balance of kinase and phosphatase activities. These sensors utilize changes in fluorescence emission of an individual fluorophore or Förster resonance energy transfer (FRET) to detect changes in second messenger concentration. cAMP and kinase activity reporter probes have provided powerful tools for the study of localized signals. Studies relying on these and related probes have the potential to further revolutionize our understanding of G protein-coupled receptor signaling systems. Unfortunately, investigators have not been able to take full advantage of the potential of these probes due to the limited signal-to-noise ratio of the probes and the limited ability of standard epifluorescence and confocal microscope systems to simultaneously measure the distributions of multiple signals (e.g. cAMP, Ca2+, and changes in kinase activities) in real time. In this review, we focus on recently implemented strategies to overcome these limitations: hyperspectral imaging and adaptive thresholding approaches to track dynamic regions of interest (ROI). This combination of approaches increases signal-to-noise ratio and contrast, and allows identification of localized signals throughout cells. These in turn lead to the identification and quantification of intracellular signals with higher effective resolution. Hyperspectral imaging and dynamic ROI tracking approaches offer investigators additional tools with which to visualize and quantify multiplexed intracellular signaling systems.
Collapse
Affiliation(s)
- Santina C Johnson
- Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
| | - Naga S Annamdevula
- Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Department of Physiology and Cell Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
| | - Silas J Leavesley
- Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Chemical and Biomolecular Engineering, University of South Alabama, Mobile, AL, U.S.A
| | - C Michael Francis
- Department of Physiology and Cell Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
| | - Thomas C Rich
- Department of Pharmacology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
- Center for Lung Biology, Frederick P. Whiddon College of Medicine, University of South Alabama, Mobile, AL, U.S.A
| |
Collapse
|
16
|
Hurter F, Halbritter ALJ, Ahmad IM, Braun M, Sigurdsson ST, Wachtveitl J. Förster resonance energy transfer within the neomycin aptamer. Phys Chem Chem Phys 2024; 26:7157-7165. [PMID: 38348887 DOI: 10.1039/d3cp05728c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Förster resonance energy transfer (FRET) measurements between two dyes is a powerful method to interrogate both structure and dynamics of biopolymers. The intensity of a fluorescence signal in a FRET measurement is dependent on both the distance and the relative orientation of the dyes. The latter can at the same time both complicate the analysis and give more detailed information. Here we present a detailed spectroscopic study of the energy transfer between the rigid FRET labels Çmf (donor) and tCnitro (quencher/acceptor) within the neomycin aptamer N1. The energy transfer originates from multiple emitting states of the donor and occurs on a low picosecond to nanosecond time-scale. To fully characterize the energy transfer, ultrafast transient absorption measurements were performed in conjunction with static fluorescence and time-correlated single photon counting (TCSPC) measurements, showing a clear distance dependence of both signal intensity and lifetime. Using a known NMR structure of the ligand-bound neomycin aptamer, the distance between the two labels was used to estimate κ2 and, therefore, make qualitative statements about the change in orientation after ligand binding with unprecedented temporal and spatial resolution. The advantages and potential applications of absorption-based methods using rigid labels for the characterization of FRET processes are discussed.
Collapse
Affiliation(s)
- Florian Hurter
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Main, Max-von-Laue-Str. 7, Frankfurt 60438, Germany.
| | - Anna-Lena J Halbritter
- Science Institute, University of Iceland, Dunhaga 3, Reykjavik 107, Iceland
- Department of Chemistry, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Iram M Ahmad
- Science Institute, University of Iceland, Dunhaga 3, Reykjavik 107, Iceland
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Main, Max-von-Laue-Str. 7, Frankfurt 60438, Germany.
| | | | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Main, Max-von-Laue-Str. 7, Frankfurt 60438, Germany.
| |
Collapse
|
17
|
Yuan Y, Di Y, Chen Y, Yu H, Li R, Yu S, Li F, Li Z, Yin Y. A fluorescent aptasensor for highly sensitive and selective detection of carcinoembryonic antigen based on upconversion nanoparticles and WS 2 nanosheets. Anal Methods 2024; 16:1225-1231. [PMID: 38314827 DOI: 10.1039/d3ay02175k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
A highly sensitive fluorescent aptasensor for carcinoembryonic antigen (CEA) was developed by employing upconversion nanoparticles (UCNPs) as an energy donor and WS2 nanosheets as an energy acceptor, respectively. Polyacrylic acid (PAA) modified NaYF4:Yb/Er UCNPs and an amine modified CEA aptamer were linked together by a covalent bond. Owing to the physical adsorption between WS2 nanosheets and the CEA aptamer, the UCNPs-aptamer was close to WS2 nanosheets, resulting in upconversion fluorescence energy transfer from UCNPs to WS2 nanosheets, and the UCNP fluorescence was quenched. With the introduction of CEA into the UCNPs-aptamer complex system, the aptamer preferentially bound to CEA resulting in a change in spatial conformation which caused UCNPs to depart from WS2 nanosheets. As a result, the energy transfer was inhibited and the fluorescence of UCNPs was observed again, and the degree of fluorescence recovery was linearly related to the concentration of CEA in a range of 0.05-10 ng mL-1 with a limit of detection of 0.008 ng mL-1. Furthermore, the aptasensor based on UCNPs and WS2 nanosheets could be competent for detecting CEA in human serum, which suggests the great application potential of the proposed aptasensor in clinical diagnosis.
Collapse
Affiliation(s)
- Yunxia Yuan
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Yi Di
- National Beverage and Grain and Oil Products Quality Inspection and Testing Center, Wuhan Product Quality Supervision & Testing Institute, Wuhan 430048, China
| | - Yuan Chen
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Huichun Yu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Ruhuan Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Songwei Yu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Fang Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Zhaozhou Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China.
| | - Yong Yin
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China.
- International Joint Laboratory of Green Food Processing, Quality and Safety Control of Henan Province, Henan University of Science and Technology, Luoyang 471023, China
| |
Collapse
|
18
|
Grabenhorst L, Sturzenegger F, Hasler M, Schuler B, Tinnefeld P. Single-Molecule FRET at 10 MHz Count Rates. J Am Chem Soc 2024; 146:3539-3544. [PMID: 38266173 DOI: 10.1021/jacs.3c13757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
A bottleneck in many studies utilizing single-molecule Förster resonance energy transfer is the attainable photon count rate, as it determines the temporal resolution of the experiment. As many biologically relevant processes occur on time scales that are hardly accessible with currently achievable photon count rates, there has been considerable effort to find strategies to increase the stability and brightness of fluorescent dyes. Here, we use DNA nanoantennas to drastically increase the achievable photon count rates and observe fast biomolecular dynamics in the small volume between two plasmonic nanoparticles. As a proof of concept, we observe the coupled folding and binding of two intrinsically disordered proteins, which form transient encounter complexes with lifetimes on the order of 100 μs. To test the limits of our approach, we also investigated the hybridization of a short single-stranded DNA to its complementary counterpart, revealing a transition path time of 17 μs at photon count rates of around 10 MHz, which is an order-of-magnitude improvement compared to the state of the art. Concomitantly, the photostability was increased, enabling many seconds long megahertz fluorescence time traces. Due to the modular nature of the DNA origami method, this platform can be adapted to a broad range of biomolecules, providing a promising approach to study previously unobservable ultrafast biophysical processes.
Collapse
Affiliation(s)
- Lennart Grabenhorst
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377 München, Germany
| | | | - Moa Hasler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
- Department of Physics, University of Zurich, 8057 Zurich, Switzerland
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, 81377 München, Germany
| |
Collapse
|
19
|
Li L, Xue Y, Li X, Li J, Fu Y, Ding Y, Liu T, Jia N, Wu Y, Bu H, Ouyang X. Copper Nanosheet-Based Wash-Free Fluorescence Imaging of Cancer Cells. Anal Chem 2024; 96:2052-2058. [PMID: 38263605 DOI: 10.1021/acs.analchem.3c04644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Near-infrared fluorescence (NIRF) probes greatly facilitate in vivo imaging of various biologically important species. However, there are several significant limitations such as consuming washing steps, photobleaching, and low signal intensity. Herein, we synthesized fluorescent copper nanosheets templated with DNA scaffolds (DNS/CuNSs). We employ them and Cy5.5 of the fluorescence resonance energy transfer (FRET) system, which have a larger Stokes shift (∼12-fold) than the traditional NIRF dye Cy5.5. Based on their excellent fluorescence properties, we employ DNS/CuNSs-Cy5.5 for fluorescence probes in cancer cell imaging. Compared with the free Cy5.5 fluorescence probe, the novel fluorescence imaging probe implements wash-free imaging and exhibits enhanced anti-photobleaching ability (∼5.5-fold). Moreover, the FRET system constructed by DNS/CuNSs has a higher signal amplification ability (∼4.17-fold), which is more similar to that of Cu nanoclusters prepared with DNA nanomonomers as a template. This work provides a new idea for cancer cell MCF-7 imaging and is expected to promote the development of cancer cell fluorescence imaging.
Collapse
Affiliation(s)
- Le Li
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Yumiao Xue
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Xinyi Li
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Jiaqi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Yue Fu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Yawen Ding
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Ting Liu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Nan Jia
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Yongli Wu
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| | - Huaiyu Bu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P. R. China
| | - Xiangyuan Ouyang
- Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, Key Laboratory of Synthetic and Natural Functional Molecule of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, Shaanxi 710127, P. R. China
| |
Collapse
|
20
|
Jung HJ, Park BH, Kim SH, Hong SC. Integrating magnetic tweezers and single-molecule FRET: A comprehensive approach to studying local and global conformational changes simultaneously. Methods Enzymol 2024; 694:167-189. [PMID: 38492950 DOI: 10.1016/bs.mie.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2024]
Abstract
This chapter presents the integration of magnetic tweezers with single-molecule FRET technology, a significant advancement in the study of nucleic acids and other biological systems. We detail the technical aspects, challenges, and current status of this hybrid technique, which combines the global manipulation and observation capabilities of magnetic tweezers with the local conformational detection of smFRET. This innovative approach enhances our ability to analyze and understand the molecular mechanics of biological systems. The chapter serves as our first formal documentation of this method, offering insights and methodologies developed in our laboratory over the past decade.
Collapse
Affiliation(s)
- Hae Jun Jung
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Department of Physics, Korea University, Seoul, Korea
| | - Beom-Hyeon Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Department of Physics, Korea University, Seoul, Korea
| | - Sook Ho Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Department of Physics, Korea University, Seoul, Korea; College of Veterinary Medicine, Chungbuk National University, Cheongju, Korea
| | - Seok-Cheol Hong
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Department of Physics, Korea University, Seoul, Korea.
| |
Collapse
|
21
|
Petutschnig EK, Pierdzig L, Mittendorf J, Niebisch JM, Lipka V. A novel fluorescent protein pair facilitates FLIM-FRET analysis of plant immune receptor interaction under native conditions. J Exp Bot 2024; 75:746-759. [PMID: 37878766 DOI: 10.1093/jxb/erad418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/24/2023] [Indexed: 10/27/2023]
Abstract
Elucidating protein-protein interactions is crucial for our understanding of molecular processes within living organisms. Microscopy-based techniques can detect protein-protein interactions in vivo at the single-cell level and provide information on their subcellular location. Fluorescence lifetime imaging microscopy (FLIM)-Förster resonance energy transfer (FRET) is one of the most robust imaging approaches, but it is still very challenging to apply this method to proteins which are expressed under native conditions. Here we describe a novel combination of fluorescence proteins (FPs), mCitrine and mScarlet-I, which is ideally suited for FLIM-FRET studies of low abundance proteins expressed from their native promoters in stably transformed plants. The donor mCitrine displays excellent brightness in planta, near-mono-exponential fluorescence decay, and a comparatively long fluorescence lifetime. Moreover, the FRET pair has a good spectral overlap and a large Förster radius. This allowed us to detect constitutive as well as ligand-induced interaction of the Arabidopsis chitin receptor components CERK1 and LYK5 in a set of proof-of-principle experiments. Due to the good brightness of the acceptor mScarlet-I, the FP combination can be readily utilized for co-localization studies. The FP pair is also suitable for co-immunoprecipitation experiments and western blotting, facilitating a multi-method approach for studying and confirming protein-protein interactions.
Collapse
Affiliation(s)
- Elena Kristin Petutschnig
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
- Central Microscopy Facility of the Faculty of Biology & Psychology, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
| | - Leon Pierdzig
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
| | - Josephine Mittendorf
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
| | - Jule Meret Niebisch
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
- Central Microscopy Facility of the Faculty of Biology & Psychology, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, D-37077 Göttingen, Germany
| |
Collapse
|
22
|
Gu J, Han T, Peng X, Kang H, Dong L. Highly sensitive fluorescent probe and portable test strip based on polyacrylic acid functionalized quantum dots for rapid visual detection of malachite green. Talanta 2024; 268:125359. [PMID: 37952316 DOI: 10.1016/j.talanta.2023.125359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/15/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Malachite green (MG) has been banned in aquaculture by many countries due to its high carcinogenicity, high teratogenicity, and easy residue. However, it is cheap and efficient characteristics have made it difficult to eliminate in recent decades, so it is essential to develop a rapid and accurate detection method for MG. Here, a highly Sensitive fluorescent probe based on polyacrylic acid (PAA) functionalized CdSe/CdxZn1-xS quantum dots (QDs) was prepared for the determination of MG. QDs functionalized by PAA (QDs@PAA) were used as energy donors, and MG was used as energy acceptor to construct fluorescence resonance energy transfer (FRET) system. The fluorescence of QDs@PAA could be linearly quenched by MG in the range of 0.05 ⁓ 2 μM, and the detection limit was 0.011 μM. In addition, a small amount of QDs@PAA (30 μL) was printed on the solid substrate by inkjet printing technology to prepare fluorescent test strips. When the concentration of MG was 2 μM, the fluorescent test strips were quenched and the detection process could be completed within 10 s, demonstrating significant potential for rapid visual detection of MG.
Collapse
Affiliation(s)
- Jiashuai Gu
- Center for Smart Materials and Devices, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, PR China
| | - Ting Han
- Center for Smart Materials and Devices, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, PR China
| | - Xiangdong Peng
- Center for Smart Materials and Devices, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, PR China
| | - Hong Kang
- Center for Smart Materials and Devices, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, PR China
| | - Lijie Dong
- Center for Smart Materials and Devices, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Luoshi Road 122, Wuhan 430070, PR China; Hainan Institute, Wuhan University of Technology, Sanya 572000, PR China.
| |
Collapse
|
23
|
Mersch SA, Bergman S, Sheets ED, Boersma AJ, Heikal AA. Two-photon excited-state dynamics of mEGFP-linker-mScarlet-I crowding biosensor in controlled environments. Phys Chem Chem Phys 2024; 26:3927-3940. [PMID: 38231116 DOI: 10.1039/d3cp04733d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Macromolecular crowding affects many cellular processes such as diffusion, biochemical reaction kinetics, protein-protein interactions, and protein folding. Mapping the heterogeneous, dynamic crowding in living cells or tissues requires genetically encoded, site-specific, crowding sensors that are compatible with quantitative, noninvasive fluorescence micro-spectroscopy. Here, we carried out time-resolved 2P-fluorescence measurements of a new mEGFP-linker-mScarlet-I macromolecular crowding construct (GE2.3) to characterize its environmental sensitivity in biomimetic crowded solutions (Ficoll-70, 0-300 g L-1) via Förster resonance energy transfer (FRET) analysis. The 2P-fluorescence lifetime of the donor (mEGFP) was measured under magic-angle polarization, in the presence (intact) and absence (enzymatically cleaved) of the acceptor (mScarlet-I), as a function of the Ficoll-70 concentration. The FRET efficiency was used to quantify the sensitivity of GE2.3 to macromolecular crowding and to determine the environmental dependence of the mEGFP-mScarlet-I distance. We also carried out time-resolved 2P-fluorescence depolarization anisotropy to examine both macromolecular crowding and linker flexibility effects on GE2.3 rotational dynamics within the context of the Stokes-Einstein model as compared with theoretical predictions based on its molecular weight. These time-resolved 2P-fluorescence depolarization measurements and conformational population analyses of GE2.3 were also used to estimate the free energy gain upon the structural collapse in crowded environment. Our results further the development of a rational engineering design for bioenvironmental sensors without the interference of cellular autofluorescence. Additionally, these results in well-defined environments will inform our future in vivo studies of genetically encoded GE2.3 towards the mapping of the crowded intracellular environment under different physiological conditions.
Collapse
Affiliation(s)
- Sarah A Mersch
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Sarah Bergman
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Erin D Sheets
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA.
| | - Arnold J Boersma
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Ahmed A Heikal
- Department of Chemistry and Biochemistry, Swenson College of Science and Engineering, University of Minnesota Duluth, Duluth, MN 55812, USA.
| |
Collapse
|
24
|
Wang Y, Luo C, Lou X, Li F, Huang Y, Xia F. Fluorescent Selectivity-Enhanced FRET Based on 3D Photonic Crystals for Multianalyte Sensing. Anal Chem 2024; 96:1630-1639. [PMID: 38217493 DOI: 10.1021/acs.analchem.3c04547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
Fluorescence resonance energy transfer (FRET) finds widespread utility in biochemical sensing, single-molecule experiments, cell physiology, and various other domains due to its inherent simplicity and high sensitivity. Nevertheless, the efficiency of energy transfer between the FRET donor and acceptor is significantly contingent on the local photonic environment, a factor that limits its application in complex systems or multianalyte detections. Here, a fluorescent selectivity-enhanced acridine orange (AO)-aflatoxins (AFs) FRET system based on a range of 3D topological photonic crystals (PCs) was developed with the aim of enhancing the selectivity and discrimination capabilities of FRET. By exploring the angle-dependent characteristics of the photonic stopband, the stopband distribution across different 3D topological PCs pixels was investigated. This approach led to selective fluorescence enhancement in PCs that matched the stopbands, enabling the successful discrimination of six distinct aflatoxins and facilitating complex multianalysis of moldy food samples. In particular, the stopband, which was strategically positioned within the blue-purple structural color range, exhibited a strong alignment with the fluorescence peaks of both the FRET donor and acceptor. This alignment allowed the 3D three-pointed star PCs to be effectively employed for the identification of mixed samples containing six distinct aflatoxins as well as the detection of real aflatoxin samples present in moldy potatoes, bread, oats, and peanuts. Impressively, this approach achieved a remarkable accuracy rate of 100%. This innovative strategy not only presents a novel avenue for developing a multitarget discrimination analysis system but also offers a convenient pretreatment method for the quantitative detection of various aflatoxins.
Collapse
Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Cihui Luo
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Xiaoding Lou
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Fengyu Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Guangdong Engineering & Technology Research Centre of Graphene-like Materials and Products, Jinan University, Guangzhou 510632, China
| | - Yu Huang
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| |
Collapse
|
25
|
Nguyen TD, Chen YI, Nguyen AT, Chen LH, Yonas S, Litvinov M, He Y, Kuo YA, Hong S, Rylander HG, Yeh HC. Multiplexed imaging in live cells using pulsed interleaved excitation spectral FLIM. Opt Express 2024; 32:3290-3307. [PMID: 38297554 PMCID: PMC11018333 DOI: 10.1364/oe.505667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/30/2023] [Accepted: 12/30/2023] [Indexed: 02/02/2024]
Abstract
Multiplexed fluorescence detection has become increasingly important in the fields of biosensing and bioimaging. Although a variety of excitation/detection optical designs and fluorescence unmixing schemes have been proposed to allow for multiplexed imaging, rapid and reliable differentiation and quantification of multiple fluorescent species at each imaging pixel is still challenging. Here we present a pulsed interleaved excitation spectral fluorescence lifetime microscopic (PIE-sFLIM) system that can simultaneously image six fluorescent tags in live cells in a single hyperspectral snapshot. Using an alternating pulsed laser excitation scheme at two different wavelengths and a synchronized 16-channel time-resolved spectral detector, our PIE-sFLIM system can effectively excite multiple fluorophores and collect their emission over a broad spectrum for analysis. Combining our system with the advanced live-cell labeling techniques and the lifetime/spectral phasor analysis, our PIE-sFLIM approach can well unmix the fluorescence of six fluorophores acquired in a single measurement, thus improving the imaging speed in live-specimen investigation.
Collapse
Affiliation(s)
- Trung Duc Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yuan-I Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Anh-Thu Nguyen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Limin H. Chen
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Siem Yonas
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Mitchell Litvinov
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yujie He
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Yu-An Kuo
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Soonwoo Hong
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - H. Grady Rylander
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
| | - Hsin-Chih Yeh
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA
- Texas Materials Institute, University of Texas at Austin, Austin, TX, USA
| |
Collapse
|
26
|
Qin D, Han Y, Jiang H, Hu L. A rhodamine coumarin-derived fluorescence probe that selectively detects Fe 3+ and measures radiation doses. Anal Methods 2024; 16:403-410. [PMID: 38164930 DOI: 10.1039/d3ay01875j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
We synthesized a fluorescence ratiometric probe by combining coumarin and rhodamine B with ethylenediamine to sense Fe3+ and measure ionizing radiation doses. The presence of Fe3+ caused rhodamine to transition from a closed helical structure to an open-ring structure. Additionally, fluorescence resonance energy transfer (FRET) occurred between coumarin and rhodamine B. As a result, the fluorescence intensity at 405 nm (I405) due to coumarin was decreased, whereas that at 585 nm (I585) derived from open-ring structure rhodamine B was increased. The ratio of I585 and I405 (I585/I405) linearly increased as the Fe3+ concentration increased. The probe sensed Fe3+ in a 0-110 μM range, with a lower limit of detection (LOD) of 0.226 μM. Inspired by Fricke dosimeters, we extended the probe to measure X-ray doses using the fluorescence methodology. The probe measured X-ray doses in a 0-30 Gy range with a lower LOD of 0.5 Gy. Additionally, the dosing capability was independent of the dosing rates. Our probe showed potential for detecting Fe3+ and measuring ionizing radiation doses.
Collapse
Affiliation(s)
- Danni Qin
- State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou, China.
| | - Yaqi Han
- State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou, China.
| | - Hao Jiang
- State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou, China.
- Key Laboratory of Polymeric Material Design and Synthesis for Biomedical Function, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou, China
| | - Liang Hu
- State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou, China.
| |
Collapse
|
27
|
Gu L, Li Y, Kong X, Zhang K, Qin Y, Zhou X, Ji H, Li G, Wu L. A stable ratiometric fluorescent probe for hypochlorous acid detection and rheumatoid arthritis evaluation. Biomater Sci 2024; 12:330-334. [PMID: 38173335 DOI: 10.1039/d3bm01576a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
A ratiometric fluorescent probe (MeO-CNPPV Pdots) based on the principle of fluorescence resonance energy transfer (FRET) was designed for hypochlorous acid (HOCl) and rheumatoid arthritis (RA) detection. The presence of HOCl can block the energy transfer from CNPPV to MeOTPATBT, resulting in a ratio change in the fluorescence of Pdots (I600 nm/I680 nm). This strategy provides a valuable paradigm in early RA evaluation.
Collapse
Affiliation(s)
- Liuwei Gu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| | - Yinghao Li
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| | - Xiaojie Kong
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| | - Ke Zhang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| | - Yuling Qin
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| | - Xiaobo Zhou
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| | - Haiwei Ji
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| | - Guo Li
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, No. 9, Seyuan Road, Nantong 226019, Jiangsu, P. R. China.
| |
Collapse
|
28
|
Li P, Luo C, Chen X, Huang C. A novel "off-on" ratiometric fluorescent aptasensor for adenosine detection based on FRET between quantum dots and graphene oxide. Spectrochim Acta A Mol Biomol Spectrosc 2024; 305:123557. [PMID: 37866265 DOI: 10.1016/j.saa.2023.123557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/30/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
A novel "off-on" ratiometric fluorescent aptasensor was established for adenosine detection based on fluorescence resonance energy transfer (FRET) between CdS QDs, DNA QDs as donor and graphene oxide (GO) as acceptor. Amino-riched DNA QDs covalently bonded to the carboxyl group on the edge of the GO, and with the absorption of the TGA-modified CdS QDs with aptamer (CdS QDs-apt) onto the GO surface via the π-π stacking interaction. The fluorescence of both CdS QDs and DNA QDs were efficiently quenched due to FRET (turn off). When adenosine was present, the specific binding of the aptamer to the target preferentially that released the CdS QDs-apt from GO. The process would inhibit the FRET which contribute to the fluorescence of CdS QDs-apt recovery again (turn on), while the fluorescence intensity of DNA QDs only slightly altered and acted as the reference signal. Thus, a novel "off-on" ratiometric fluorescent aptasensor for adenosine detection was constructed accordingly. There was a good linearity relationship between the ratio of the FL intensity (F595 nm/F464 nm) and the concentration of adenosine in the range of 20.00-180.0 nmol/L with a detection limit of 1.3 nmol/L (S/N = 3, n = 9). Importantly, the feasibility of the developed aptasensor for selective detection of adenosine in serum and urine samples with satisfactory results. The recoveries were observed to be 97.04-100.2 %.
Collapse
Affiliation(s)
- Pu Li
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Chen Luo
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaoxiao Chen
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Chaobiao Huang
- Xingzhi College, Zhejiang Normal University, Lanxi 321100, China; College of Chemistry and Life Science, Zhejiang Normal University, Jinhua 321004, China.
| |
Collapse
|
29
|
Bonilla PA, Shrestha R. FLIM-FRET Protein-Protein Interaction Assay. Methods Mol Biol 2024; 2797:261-269. [PMID: 38570466 DOI: 10.1007/978-1-0716-3822-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Fluorescence lifetime imaging performed under FRET conditions between two interacting molecules is a sensitive and robust way to quantify intermolecular interactions in cells. The fluorescence lifetime, an inherent property of the fluorophore, remains unaffected by factors such as concentration, laser intensity, and other photophysical artifacts. In the context of FLIM-FRET, the focus lies on measuring the fluorescence lifetime of the donor molecule, which diminishes upon interaction with a neighboring acceptor molecule. In this study, we present a step-by-step experimental protocol for applying FLIM-FRET to investigate protein-protein interactions involving various RAS isoforms and RAS effectors at the live cell's plasma membrane. By utilizing the FRET pair comprising enhanced green fluorescent protein (eGFP) and fluorescent mCherry, we demonstrate that the proximity and possible nanoclustering of eGFP-tagged KRAS4b G12D and mCherry-tagged KRAS4b WT led to a reduction in the donor eGFP's fluorescence lifetime. The donor lifetime of eGFP-tagged KRAS decreases even further when treated with a dimer-inducing small molecule, or in the presence of RAF proteins, suggesting a greater FRET efficiency, and thus less distance, between donor and acceptor.
Collapse
Affiliation(s)
- Pedro Andrade Bonilla
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rebika Shrestha
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| |
Collapse
|
30
|
Lalitha R, Velmathi S. A Study of Small Molecule-Based Rhodamine-Derived Chemosensors and their Implications in Environmental and Biological Systems from 2012 to 2021: Latest Advancement and Future Prospects. J Fluoresc 2024; 34:15-118. [PMID: 37212978 DOI: 10.1007/s10895-023-03231-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/28/2023] [Indexed: 05/23/2023]
Abstract
Rhodamine-based chemosensors have sparked considerable interest in recent years due to their remarkable photophysical properties, which include high absorption coefficients, exceptional quantum yields, improved photostability, and significant red shifts. This article presents an overview of the diverse fluorometric, and colorimetric sensors produced from rhodamine, as well as their applications in a wide range of fields. The ability of rhodamine-based chemosensors to detect a wide range of metal ions, including Hg+2, Al3+, Cr3+, Cu2+, Fe3+, Fe2+, Cd2+, Sn4+, Zn2+, and Pb2+, is one of their major advantages. Other applications of these sensors include dual analytes, multianalytes, and relay recognition of dual analytes. Rhodamine-based probes can also detect noble metal ions such as Au3+, Ag+, and Pt2+. They have been used to detect pH, biological species, reactive oxygen and nitrogen species, anions, and nerve agents in addition to metal ions. The probes have been engineered to undergo colorimetric or fluorometric changes upon binding to specific analytes, rendering them highly selective and sensitive by ring-opening via different mechanisms such as Photoinduced Electron Transfer (PET), Chelation Enhanced Fluorescence (CHEF), Intramolecular Charge Transfer (ICT), and Fluorescence Resonance Energy Transfer (FRET). For improved sensing performance, light-harvesting dendritic systems based on rhodamine conjugates has also been explored for enhanced sensing performance. These dendritic arrangements permit the incorporation of numerous rhodamine units, resulting in an improvement in signal amplification and sensitivity. The probes have been utilised extensively for imaging biological samples, including imaging of living cells, and for environmental research. Moreover, they have been combined into logic gates for the construction of molecular computing systems. The usage of rhodamine-based chemosensors has created significant potential in a range of disciplines, including biological and environmental sensing as well as logic gate applications. This study focuses on the work published between 2012 and 2021 and emphasises the enormous research and development potential of these probes.
Collapse
Affiliation(s)
- Raguraman Lalitha
- Organic and Polymer Synthesis Laboratory, Department of Chemistry, National Institute of Technology, Tiruchirappalli, 620 015, India
| | - Sivan Velmathi
- Organic and Polymer Synthesis Laboratory, Department of Chemistry, National Institute of Technology, Tiruchirappalli, 620 015, India.
| |
Collapse
|
31
|
Vermeer B, van Ossenbruggen J, Schmid S. Single-Molecule FRET-Resolved Protein Dynamics - from Plasmid to Data in Six Steps. Methods Mol Biol 2024; 2694:267-291. [PMID: 37824009 DOI: 10.1007/978-1-0716-3377-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for the detection of conformational dynamics of biomolecules. While many smFRET experiments are performed using dye-labeled DNA, here we describe a comprehensive protocol to resolve the conformational dynamics of a protein system - notably from plasmid to data. Using the example of the heat-shock protein Hsp90, we describe the protein production and threefold site-specific bioconjugation, the smFRET measurement using total internal reflection fluorescence microscopy (TIRFM), and raw data processing to reveal time-resolved protein dynamics. The described smFRET approach is readily transferrable to the study of many more all-protein systems and their conformational energy landscape.
Collapse
Affiliation(s)
- Benjamin Vermeer
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Sonja Schmid
- Laboratory of Biophysics, Wageningen University & Research, Wageningen, The Netherlands.
| |
Collapse
|
32
|
Ouyang Q, Rong Y, Wang B, Ahmad W, Liu S, Chen Q. An innovative solid-phase biosensor for rapid on-site detection of N-nitrosodimethylamine incorporating zein film and upconversion nanoparticles. Food Chem 2024; 430:136981. [PMID: 37541034 DOI: 10.1016/j.foodchem.2023.136981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 08/06/2023]
Abstract
Pickled frequently contains nitrosodimethylamine (NDMA), a mutagenic and carcinogenic substance that is dangerous for the general public's health. This study reports on the fabrication of a fluorescent biosensor using zein film and aptamer functionalized upconversion nanoparticles (UCNPs) for on-site monitoring of NDMA in meat. UCNPs were first prepared followed by aptamer binding and mixing with zein film, which was further conjugated with cDNA of dabcyl modified at 5'. The fluorescence resonance energy transfer (FRET) mechanism between the UCNPs and dabcyl was exploited. The fluorescence signals of the zein film recovered when NDMA was present because it was selectively collected by the particular aptamer and damaged the cDNA structure. The designed functionalized zein film was used for on-site and portable determination of NDMA with a lower limit of detection of 0.017 ng/mL, and possessed a satisfactory recovery ranging from 95.8% to 100.2% with no significant difference compared with the GC-MS method.
Collapse
Affiliation(s)
- Qin Ouyang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China.
| | - Yanna Rong
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Baoning Wang
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Waqas Ahmad
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Shuangshuang Liu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Quansheng Chen
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China.
| |
Collapse
|
33
|
Abstract
Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon that has been repurposed as a biophysical tool to measure nanometer distances. With FRET by DNA eXchange, or FRET X, many points of interest (POIs) in a single object can be probed, overcoming a major limitation of conventional single-molecule FRET. In FRET X, short fluorescently labeled DNA imager strands specifically and transiently bind their complementary docking strands on a target molecule, such that at most a single FRET pair is formed at each point in time and multiple POIs on a single molecule can be readily probed. Here, we describe the sample preparation, image acquisition, and data analysis for structural analysis of DNA nanostructures with FRET X.
Collapse
Affiliation(s)
- Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Raman van Wee
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
| |
Collapse
|
34
|
Larsen EK, Abreu-Blanco M, Rabara D, Stephen AG. KRAS4b:RAF-1 Homogenous Time-Resolved Fluorescence Resonance Energy Transfer Assay for Drug Discovery. Methods Mol Biol 2024; 2797:159-175. [PMID: 38570459 DOI: 10.1007/978-1-0716-3822-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Homogenous time-resolved FRET (HTRF) assays have become one of the most popular tools for pharmaceutical drug screening efforts over the last two decades. Large Stokes shifts and long fluorescent lifetimes of lanthanide chelates lead to robust signal to noise, as well as decreased false positive rates compared to traditional assay techniques. In this chapter, we describe an HTRF protein-protein interaction (PPI) assay for the KRAS4b G-domain in the GppNHp-bound state and the RAF-1-RBD currently used for drug screens. Application of this assay contributes to the identification of lead compounds targeting the GTP-bound active state of K-RAS.
Collapse
Affiliation(s)
- Erik K Larsen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Maria Abreu-Blanco
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Dana Rabara
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| |
Collapse
|
35
|
van den Wildenberg SMJL, Prevo B, Peterman EJG. A Brief Introduction to Single-Molecule Fluorescence Methods. Methods Mol Biol 2024; 2694:111-132. [PMID: 37824002 DOI: 10.1007/978-1-0716-3377-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
One of the most popular single-molecule approaches in biological science is single-molecule fluorescence microscopy, which will be the subject of the following section of this volume. Fluorescence methods provide the sensitivity required to study biology on the single-molecule level, but they also allow access to useful measurable parameters on time and length scales relevant for the biomolecular world. Before several detailed experimental approaches will be addressed, we will first give a general overview of single-molecule fluorescence microscopy. We start with discussing the phenomenon of fluorescence in general and the history of single-molecule fluorescence microscopy. Next, we will review fluorescent probes in more detail and the equipment required to visualize them on the single-molecule level. We will end with a description of parameters measurable with such approaches, ranging from protein counting and tracking, single-molecule localization super-resolution microscopy, to distance measurements with Förster resonance energy transfer and orientation measurements with fluorescence polarization.
Collapse
Affiliation(s)
- Siet M J L van den Wildenberg
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Université Clermont Auvergne, CNRS, IRD, OPGC, Laboratoire Magmas et Volcans, Clermont-Ferrand, France
- Université Clermont Auvergne, CNRS/IN2P3, Laboratoire de Physique de Clermont, Clermont-Ferrand, France
| | - Bram Prevo
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
36
|
Che D, Cao X, Chen C, Yan H. A point-of-care aptasensor based on the upconversion nanoparticles/MoS 2 FRET system for the detection of Pseudomonas aeruginosa infection. Mikrochim Acta 2023; 191:61. [PMID: 38157041 DOI: 10.1007/s00604-023-06155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024]
Abstract
The rapid detection of Pseudomonas aeruginosa (P. aeruginosa) is of great significance for the diagnosis of medical infection. In view of the above, a novel aptasensor based on fluorescence resonance energy transfer (FRET) was developed. It contained aptamer-coupled upconversion nanoparticles (UCNPs-apt) as a donor (excitation 980 nm) and molybdenum disulfide (MoS2) nanosheets as an acceptor. The upconversion fluorescence aptamer system was investigated to obtain the optimal parameters of MoS2 concentration, the incubation time of UCNPs-apt/MoS2 and P. aeruginosa, and pH. Based on the optimal parameters, a linear calibration equation (emission 654 nm) with a wide detection range 8.7 × 10 ~ 8.7 × 107 cfu/mL, a high coefficient of determination R2 0.9941, and a low limit of determination (LOD) 15.5 cfu/mL were established. The method was validated with P. aeruginosa infected foci of mouse wound. The advantage of this aptasensor is that analysis results can be obtained within 1.5 h, which was much faster than that of the standard method (18-24 h). Furthermore, combined with a portable instrument, it can be used as a point-of-care testing for the early detection of P. aeruginosa infection, which is useful for selecting the correct antibiotics to achieve good therapeutic effects. Additionally, it also has a broad application prospect in food and environmental areas.
Collapse
Affiliation(s)
- Dou Che
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Xitao Cao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Chong Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China
| | - Hui Yan
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, China.
| |
Collapse
|
37
|
Higuera-Rodriguez RA, De Pascali MC, Aziz M, Sattler M, Rant U, Kaiser W. Kinetic FRET Assay to Measure Binding-Induced Conformational Changes of Nucleic Acids. ACS Sens 2023; 8:4597-4606. [PMID: 38060303 PMCID: PMC10749467 DOI: 10.1021/acssensors.3c01527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/27/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The interaction of small molecules or proteins with RNA or DNA often involves changes in the nucleic acid (NA) folding and structure. A biophysical characterization of these processes helps us to understand the underlying molecular mechanisms. Here, we propose kinFRET (kinetics Förster resonance energy transfer), a real-time ensemble FRET methodology to measure binding and folding kinetics. With kinFRET, the kinetics of conformational changes of NAs (DNA or RNA) upon analyte binding can be directly followed via a FRET signal using a chip-based biosensor. We demonstrate the utility of this approach with two representative examples. First, we monitored the conformational changes of different formats of an aptamer (MN19) upon interaction with small-molecule analytes. Second, we characterized the binding kinetics of RNA recognition by tandem K homology (KH) domains of the human insulin-like growth factor II mRNA-binding protein 3 (IMP3), which reveals distinct kinetic contributions of the two KH domains. Our data demonstrate that kinFRET is well suited to study the kinetics and conformational changes of NA-analyte interactions.
Collapse
Affiliation(s)
- R. Anahi Higuera-Rodriguez
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Mareike C. De Pascali
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Masood Aziz
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Helmholtz
Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg 85764, Germany
| | - Michael Sattler
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Helmholtz
Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg 85764, Germany
| | - Ulrich Rant
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Wolfgang Kaiser
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| |
Collapse
|
38
|
Fischermeier D, Steinmetzger C, Höbartner C, Mitrić R. Conformational preferences of modified nucleobases in RNA aptamers and their effect on Förster resonant energy transfer. Phys Chem Chem Phys 2023; 26:241-248. [PMID: 38054366 DOI: 10.1039/d3cp04704k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Förster resonant energy transfer (FRET) can be utilized in the study of tertiary structures of RNA aptamers, which bind specific fluorophoric ligands to form a fluorogenic aptamer complex. By introducing the emissive nucleobase analog 4-cyanoindole into the fluorogenic Chili RNA aptamer a FRET pair was established. The interpretation of studies aiming to investigate those tertiary structures using FRET, however, relies on prior knowledge about conformational properties of the nucleobase, which govern exciton transfer capabilities. Herein we employed classical molecular dynamics combined with Förster exciton theory to elucidate the preferred orientation relative to proximate bases and the influence on exciton transfer efficiency in multiple substitution sites. We did this by comparing the chromophoric distances emergent from MD simulations with experimental FRET data based on structural data of the native aptamer. We present the outlined methodology as a means to reliably evaluate future nucleobase analogue candidates in terms of their structural behavior and emergent exciton transfer properties as exemplified in the study of the preferred orientation of 4-cyanoindole in the Chili RNA aptamer.
Collapse
Affiliation(s)
- David Fischermeier
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Christian Steinmetzger
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Claudia Höbartner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Roland Mitrić
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
| |
Collapse
|
39
|
Wang J, Maeda E, Tsujimura Y, Abe T, Kiyonari H, Kitaguchi T, Yokota H, Matsumoto T. In situ FRET measurement of cellular tension using conventional confocal laser microscopy in newly established reporter mice expressing actinin tension sensor. Sci Rep 2023; 13:22729. [PMID: 38123655 PMCID: PMC10733408 DOI: 10.1038/s41598-023-50142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
FRET-based sensors are utilized for real-time measurements of cellular tension. However, transfection of the sensor gene shows low efficacy and is only effective for a short period. Reporter mice expressing such sensors have been developed, but sensor fluorescence has not been measured successfully using conventional confocal microscopy. Therefore, methods for spatiotemporal measurement of cellular tension in vivo or ex vivo are still limited. We established a reporter mouse line expressing FRET-based actinin tension sensors consisting of EGFP as the donor and mCherry as the acceptor and whose FRET ratio change is observable with confocal microscopy. Tension-induced changes in FRET signals were monitored in the aorta and tail tendon fascicles, as well as aortic smooth muscle cells isolated from these mice. The pattern of FRET changes was distinctive, depending on tissue type. Indeed, aortic smooth muscle cells exhibit different sensitivity to macroscopic tensile strain in situ and in an isolated state. This mouse strain will enable novel types of biomechanical investigations of cell functions in important physiological events.
Collapse
Affiliation(s)
- Junfeng Wang
- Biomechanics Laboratory, Department of Mechanical Systems Engineering, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan
| | - Eijiro Maeda
- Biomechanics Laboratory, Department of Mechanical Systems Engineering, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan
| | - Yuki Tsujimura
- RIKEN Center for Advanced Photonics, RIKEN, Wako, Saitama, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Hideo Yokota
- RIKEN Center for Advanced Photonics, RIKEN, Wako, Saitama, Japan
| | - Takeo Matsumoto
- Biomechanics Laboratory, Department of Mechanical Systems Engineering, Graduate School of Engineering, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8603, Japan.
| |
Collapse
|
40
|
Navarro G, Sotelo E, Raïch I, Loza MI, Brea J, Majellaro M. A Robust and Efficient FRET-Based Assay for Cannabinoid Receptor Ligands Discovery. Molecules 2023; 28:8107. [PMID: 38138600 PMCID: PMC10745346 DOI: 10.3390/molecules28248107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The identification of new modulators for Cannabinoid Receptors (CBRs) has garnered significant attention in drug discovery over recent years, owing to their manifold pathophysiological implications. In the context of hit identification, the availability of robust and sensitive high-throughput screening assays is essential to enhance the likelihood of success. In this study, we present the development and validation of a Tag-lite® binding assay designed for screening hCB1/hCB2 binding, employing a dual fluorescent ligand, CELT-335. Representative ligands for CBRs, exhibiting diverse affinity and functional profiles, were utilized as reference compounds to validate the robustness and efficiency of the newly developed Tag-lite® binding assay protocol. The homogeneous format, coupled with the sensitivity and optimal performance of the fluorescent ligand CELT-335, establishes this assay as a viable and reliable method for screening in hit and lead identification campaigns.
Collapse
Affiliation(s)
- Gemma Navarro
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain
- Institute of Neuroscience of the University of Barcelona, 08035 Barcelona, Spain
| | - Eddy Sotelo
- Department of Organic Chemistry, Center for Research in Biological Chemistry and Molecular Materials (CiQUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Iu Raïch
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona, 08028 Barcelona, Spain
- Institute of Neuroscience of the University of Barcelona, 08035 Barcelona, Spain
| | - María Isabel Loza
- Research Center in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Jose Brea
- Research Center in Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Maria Majellaro
- Celtarys Research SL, Avda. Mestre Mateo, 2, 15706 Santiago de Compostela, Spain
| |
Collapse
|
41
|
Liu S, Zhao X, Ma Q, Wang G, Hou S, Ma Y, Lian Y. An ICT-FRET-based ratiometric fluorescent probe for hydrogen polysulfide based on a coumarin-naphthalimide derivative. Spectrochim Acta A Mol Biomol Spectrosc 2023; 302:123041. [PMID: 37354859 DOI: 10.1016/j.saa.2023.123041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/28/2023] [Accepted: 06/17/2023] [Indexed: 06/26/2023]
Abstract
Hydrogen polysulfide (H2Sn, n > 1), as one of the important members of reactive sulfur species (RSS), plays a vital part in the processes of both their physiology and pathology. In this work, a ratiometric fluorescent probe for H2Sn had been designed and prepared based on the combination mechanism of intramolecular charge transfer (ICT) and fluorescence resonance energy transfer (FRET). The probe chose a coumarin derivative as the energy donor, a naphthalimide derivative as the energy acceptor and 2-fluoro-5-nitrobenzoate as the H2Sn recognition group. When H2Sn was not present in the system, the ICT process of the naphthalimide acceptor was inhibited and the FRET process from the coumarin donor to the naphthalimide acceptor was turned off. When H2Sn was added, both ICT and FRET occurred due to the nucleophilic substitution-cyclization reactions between the probe and hydrogen polysulfide. In addition, the ratio value of the emission intensities at 550 nm and 473 nm (I550 nm/I473 nm) of this probe had a good linear relationship with H2Sn concentration in the range of 6.0 × 10-7-5.0 × 10-5 mol·L-1, and a detection limit of 1.8 × 10-7 mol·L-1 was obtained. The developed probe had high selectivity and sensitivity, as well as good biocompatibility. Additionally, the probe had been used to successfully image both indigenous and exogenous hydrogen polysulfide in A549 cells using confocal microscope.
Collapse
Affiliation(s)
- Shuangyu Liu
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Xuan Zhao
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Qiujuan Ma
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Engineering Research Center of Modern Chinese Medicine Research, Development and Application, Zhengzhou 450046, China.
| | - Gege Wang
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Shuqi Hou
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yijie Ma
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Yujie Lian
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou 450046, China
| |
Collapse
|
42
|
Arora A, Sharma K, Tripathi SK. Impact of luminescent MoSe 2 quantum dots on activity of trypsin under different pH environment. Spectrochim Acta A Mol Biomol Spectrosc 2023; 302:122958. [PMID: 37406547 DOI: 10.1016/j.saa.2023.122958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/20/2023] [Accepted: 05/29/2023] [Indexed: 07/07/2023]
Abstract
It is vital that a straightforward detection approach for trypsin should be developed as it is important diagnostic tool for a number of diseases. Herein, the impact of luminescent MoSe2 quantum dots on trypsin activity under different pH environment has been studied. Addition of trypsin to MoSe2 quantum dots enhanced the fluorescence of quantum dots whereas quantum dots resulted in quenching of fluorescence of trypsin. The quenching behavior at various pH and temperature was examined and revealed that the MoSe2-trypsin complex stabilized through the electrostatic interactions. The obtained negative values of zeta potential of the complex -0.11 mV, -0.30 mV and -0.59 mV for pH 6.0,7.6 and 9.0 respectively confirmed the stability of the complex. The separation between the donor and acceptor atoms in energy transfer mechanism was found to decrease (1.48 nm to 1.44 nm to 1.30 nm) with increasing value of pH. It was also evident that trypsin retained its enzyme activity in the trypsin-MoSe2 complex and under different pH environment. The Vant Hoff plot from quenching revealed 1 binding site for quantum dots by trypsin for all pH of buffer solution. The complex formation of trypsin-MoSe2 quantum dots was verified for the first time using fluorescence spectroscopy and it revealed that tryspin form complex with MoSe2 quantum dots through electrostatic interactions. Our results revealed that the MoSe2 quantum dots stabilized and sheltered the active sites of trypsin, which was likely the cause of the increased bioavailability of MoSe2 quantum dots in enzymes.
Collapse
Affiliation(s)
- Anmol Arora
- Centre of Advanced Study in Physics, Department of Physics, Panjab University, Chandigarh 160014, India
| | - Kriti Sharma
- Department of Physics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32-C, Chandigarh 160030, India.
| | - S K Tripathi
- Centre of Advanced Study in Physics, Department of Physics, Panjab University, Chandigarh 160014, India.
| |
Collapse
|
43
|
Hu J, Zhang YT, Han Y, Ma F, Li CZ, Cui L, Zhang CY. Methylation-Powered Assembly of a Single Quantum Dot-Based FRET Nanosensor for Antibody-Free and Enzyme-Free Monitoring of Locus-Specific N6-Methyladenosine in Clinical Tissues. Anal Chem 2023; 95:17945-17953. [PMID: 38000786 DOI: 10.1021/acs.analchem.3c04571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
Abstract
N6-Methyladenosine (m6A) is the most pervasive and evolutionarily conserved epitranscriptomic modification in long noncoding RNA (lncRNA), and its dysregulation may induce aberrant transcription and translation programs. Herein, we demonstrate the methylation-powered assembly of a single quantum dot (QD)-based fluorescence resonance energy transfer (FRET) nanosensor for antibody- and enzyme-free monitoring of locus-specific m6A in clinical tissues. The m6A-sensitive DNAzyme VMC10 is employed to identify a specific m6A site in lncRNA, and it catalyzes the hydrolytic cleavage of unmethylated lncRNA. The cleaved lncRNA fails to trigger the subsequent catalytic hairpin assembly (CHA) reaction due to the energy barrier. In contrast, when m6A-lncRNA is present, the methyl group in m6A protects lncRNA from VMC10-mediated cleavage. With the aid of an assistant probe, the retained intact m6A-lncRNA is released from the VMC10/lncRNA complex and subsequently triggers the CHA reaction, generating abundant AF647/biotin dual-labeled duplexes. The assembly of AF647/biotin dual-labeled duplexes onto 605QD results in efficient FRET between 605QD and AF647. The FRET signal can be simply quantified by single-molecule detection. Notably, this assay can be implemented in an antibody-free and enzyme-free manner. This nanosensor can sensitively quantify target m6A with a detection limit of 0.47 fM, and it can discriminate as low as a 0.001% m6A level from excess coexisting counterparts. Importantly, this nanosensor can monitor the cellular m6A level with single-cell sensitivity and profile target m6A expression in breast cancer and healthy para-cancerous tissues, providing a powerful tool for studying the physiological and pathological functions of m6A.
Collapse
Affiliation(s)
- Jinping Hu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Ya-Ting Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chen-Zhong Li
- Biomedical Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Lin Cui
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| |
Collapse
|
44
|
Sekhon H, Ha JH, Presti MF, Procopio SB, Jarvis AR, Mirsky PO, John AM, Loh SN. Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells. Nat Methods 2023; 20:1920-1929. [PMID: 37945909 DOI: 10.1038/s41592-023-02065-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023]
Abstract
A grand challenge in biosensor design is to develop a single-molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Here, we created a family of adaptable, turn-on maturation (ATOM) biosensors consisting of a monobody (circularly permuted at one of two positions) or a nanobody (circularly permuted at one of three positions) inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells coexpressing cyan, yellow and red ATOM sensors detected biosensor targets that were specifically localized to various subcellular compartments. Fluorescence activation involved ligand-dependent chromophore maturation with turn-on ratios of up to 62-fold in cells and 100-fold in vitro. Endoplasmic reticulum- and mitochondria-localized ATOM sensors detected ligands that were targeted to those organelles. The ATOM design was validated with three monobodies and one nanobody inserted into distinct fluorescent proteins, suggesting that customized ATOM sensors can be generated quickly.
Collapse
Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Spencer B Procopio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ava R Jarvis
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Paige O Mirsky
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Anna M John
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
| |
Collapse
|
45
|
Vela-Rodríguez C, Scarpulla I, Ashok Y, Lehtiö L. Discovery of DTX3L inhibitors through a homogeneous FRET-based assay that monitors formation and removal of poly-ubiquitin chains. SLAS Discov 2023; 28:365-375. [PMID: 37579950 DOI: 10.1016/j.slasd.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Ubiquitination is a reversible protein post-translational modification in which consequent enzymatic activity results in the covalent linking of ubiquitin to a target protein. Once ubiquitinated, a protein can undergo multiple rounds of ubiquitination on multiple sites or form poly-ubiquitin chains. Ubiquitination regulates various cellular processes, and dysregulation of ubiquitination has been associated with more than one type of cancer. Therefore, efforts have been carried out to identify modulators of the ubiquitination cascade. Herein, we present the development of a FRET-based assay that allows us to monitor ubiquitination activity of DTX3L, a RING-type E3 ubiquitin ligase. Our method shows a good signal window with a robust average Z' factor of 0.76 on 384-well microplates, indicating a good assay for screening inhibitors in a high-throughput setting. From a validatory screening experiment, we have identified the first molecules that inhibit DTX3L with potencies in the low micromolar range. We also demonstrate that the method can be expanded to study deubiquitinases, such as USP28, that reduce FRET due to hydrolysis of fluorescent poly-ubiquitin chains.
Collapse
Affiliation(s)
- Carlos Vela-Rodríguez
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Ilaria Scarpulla
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Yashwanth Ashok
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.
| |
Collapse
|
46
|
Behnam MAM, Basché T, Klein CDP. 2,2'-Bithiophene as sensor tag for ligand-protein binding assays based on Förster resonance energy transfer. Anal Biochem 2023; 682:115335. [PMID: 37777080 DOI: 10.1016/j.ab.2023.115335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/15/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023]
Abstract
Ligand-protein binding assays based on intrinsic protein fluorescence are straightforward, inexpensive methods to study ligand-protein interactions. However, their applicability is limited to ligands that can interfere with protein emission. In this Note, we describe the applicability of 2,2'-bithiophene as a FRET-based sensor tag, that can be incorporated into high-affinity ligands to generate target-specific compounds able to quench protein fluorescence upon binding. The generated ligands were assessed in different assay designs. Considerations to account for possible sources of interference with the assay readout are addressed, besides interpretation of the obtained results.
Collapse
Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Thomas Basché
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany
| | - Christian D P Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.
| |
Collapse
|
47
|
Barton JC, Anderson C, Miranda FZ, Kelley R, Kremer Hovinga JA, Terrell D, Vesely SK, George JN, Muia J. Cattle-FRETS71, a novel fluorogenic substrate with broad applicability for characterizing ADAMTS13 properties and function. J Thromb Haemost 2023; 21:3393-3401. [PMID: 37633642 PMCID: PMC10840809 DOI: 10.1016/j.jtha.2023.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 08/14/2023] [Accepted: 08/15/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND Current ADAMTS13 activity assays are important for diagnosing thrombotic thrombocytopenic purpura (TTP) but are unreliable to assay ADAMTS13 activity in animal models. The Cattle-FRETS71 assay is capable of detecting ADAMTS13 activity in plasma from multiple animal species, making it a potentially useful reagent at all stages of clinical research. The performance of Cattle-FRETS71 in TTP diagnosis is not yet known. OBJECTIVES We evaluated the performance of the Cattle-FRETS71 substrate against the human FRETS-rVWF71 and the FRETS-VWF73 commercial substrates in human plasma and serum samples to validate its utility in diagnosing TTP in patients. METHODS Internal validation was performed using heparinized plasma samples (n = 81). External validation was a blinded study using serum samples from the Oklahoma TTP Registry (n = 118, collected 2004-2014) that had been initially assayed by FRETS-VWF73 within 1 year of collection. Additional validation was performed with citrated plasma samples with variable ADAMTS13 activities (n = 32) that were analyzed by FRETS-VWF73. RESULTS There was an excellent correlation (r = 0.94) between Cattle-FRETS71 and FRETS-rVWF71 for assayed heparinized plasma samples (n = 81). Assay results between Cattle-FRETS71 and FRETS-VWF73 of Oklahoma TTP Registry serum samples (n = 118) and citrated plasma samples (n = 32) were comparably good (r = 0.81 and r = 0.85, respectively). CONCLUSION The Cattle-FRETS71 assay is comparable with other assays in quantifying ADAMTS13 activity in human plasma collected from patients with documented or suspected TTP. The versatility of Cattle-FRETS71, combined with its specificity and sensitivity, makes it a useful tool for the standardization of ADAMTS13 activity across basic and clinical research paradigms.
Collapse
Affiliation(s)
- John Cameron Barton
- Oklahoma State University College of Osteopathic Medicine, Tulsa, Oklahoma, USA
| | - Cooper Anderson
- Oklahoma State University College of Osteopathic Medicine at the Cherokee Nation, Tahlequah, Oklahoma, USA
| | - Frida Z Miranda
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, USA
| | - Rachel Kelley
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Johanna A Kremer Hovinga
- Department of Hematology and Central Hematological Laboratory, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Deirdra Terrell
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Sara K Vesely
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - James N George
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Joshua Muia
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, Oklahoma, USA.
| |
Collapse
|
48
|
Han Y, Yang J, Li Y, Chen Y, Ren H, Ding R, Qian W, Ren K, Xie B, Deng M, Xiao Y, Chu J, Zou P. Bright and sensitive red voltage indicators for imaging action potentials in brain slices and pancreatic islets. Sci Adv 2023; 9:eadi4208. [PMID: 37992174 PMCID: PMC10664999 DOI: 10.1126/sciadv.adi4208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
Genetically encoded voltage indicators (GEVIs) allow the direct visualization of cellular membrane potential at the millisecond time scale. Among these, red-emitting GEVIs have been reported to support multichannel recordings and manipulation of cellular activities with reduced autofluorescence background. However, the limited sensitivity and dimness of existing red GEVIs have restricted their applications in neuroscience. Here, we report a pair of red-shifted opsin-based GEVIs, Cepheid1b and Cepheid1s, with improved dynamic range, brightness, and photostability. The improved dynamic range is achieved by a rational design to raise the electrochromic Förster resonance energy transfer efficiency, and the higher brightness and photostability are approached with separately engineered red fluorescent proteins. With Cepheid1 indicators, we recorded complex firings and subthreshold activities of neurons on acute brain slices and observed heterogeneity in the voltage‑calcium coupling on pancreatic islets. Overall, Cepheid1 indicators provide a strong tool to investigate excitable cells in various sophisticated biological systems.
Collapse
Affiliation(s)
- Yi Han
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Junqi Yang
- Peking University–Tsinghua University–National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yuan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Chinese Institute for Brain Research (CIBR), Beijing 102206, China
| | - Yu Chen
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Huixia Ren
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Ran Ding
- Institute for Translational Neuroscience of the Second Affiliated Hospital of Nantong University, Center for Neural Developmental and Degenerative Research of Nantong University, Nantong 226001, China
| | - Weiran Qian
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Keyuan Ren
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Beichen Xie
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Mengying Deng
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yinghan Xiao
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jun Chu
- Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
- Peking University–Tsinghua University–National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Chinese Institute for Brain Research (CIBR), Beijing 102206, China
| |
Collapse
|
49
|
Yang C, Li F, Mo L, Lin W. Self-assembly of molecular beacons through metal ion coordination for fluorescence imaging of miRNA in living cells. LUMINESCENCE 2023; 38:1977-1983. [PMID: 37555579 DOI: 10.1002/bio.4573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/13/2023] [Accepted: 03/19/2023] [Indexed: 08/10/2023]
Abstract
Fluorescence nanosensors based on functional nucleic acids have been explored as a powerful sensing platform for disease-relevant miRNAs. This work developed a new hybrid nanosensor (Zr-B) through coordination-driven self-assembly of Zr ions and beacons. The prepared nanosensor exhibited high loading efficiency of beacons and could achieve sensitive and specific detection for miRNAs. The hybrid nanosensor could transfer beacons into living cells efficiently and maintain high stability and biocompatibility in the biological environment, achieving effective miRNA fluorescence imaging in living cells. Therefore, the resultant nanosensor holds potential for applications in disease diagnostics.
Collapse
Affiliation(s)
- Chan Yang
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, China
| | - Fenfen Li
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, China
| | - Liuting Mo
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, China
| | - Weiying Lin
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi, China
| |
Collapse
|
50
|
Mia AK, Bora A, Hossain MT, Sinha S, Giri PK. Fast detection of Staphylococcus aureus using thiol-functionalized WS 2 quantum dots and Bi 2O 2Se nanosheets hybrid through a fluorescence recovery mechanism. J Mater Chem B 2023; 11:10206-10217. [PMID: 37853818 DOI: 10.1039/d3tb01465g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Ultrafast and sensitive detection of Staphylococcus aureus (S. aureus), a harmful Gram-positive human pathogenic bacterium, by two-dimensional layered materials continues to be a challenge. Herein, we have studied the sensing of S. aureus using a tungsten disulfide (WS2) quantum dot (QD) and bismuth oxyselenide (Bi2O2Se) nanosheet (NS) hybrid through their unique optical functionalities. The WS2 QDs of a mean diameter of 2.5 nm were synthesized by liquid exfoliation. Due to the quantum confinement and functional groups, the WS2 QDs exhibit high fluorescence (FL) yield under UV excitation. The addition of Bi2O2Se NSs resulted in the adsorption of WS2 QDs on their surface, resulting in quenching of the FL emission due to nonfluorescent complex formation between the WS2 QDs and Bi2O2Se NSs. A specific sequencing single-standard DNA (ssDNA) aptamer, which identifies and explicitly binds with S. aureus, was attached to the defect sites of the WS2 QDs for selective detection. The thiol-modified ssDNA aptamers attach covalently to the WS2 QD defect sites, which was confirmed by Raman and X-ray photoelectron spectroscopy (XPS). The interaction of S. aureus with the aptamer functionalized WS2 QDs weakens the van der Waals interaction between the WS2 QDs and Bi2O2Se NSs, which results in the detachment of the WS2 QDs from the Bi2O2Se NS surface and restores the FL intensity of the WS2 QDs, thus allowing the efficient detection of S. aureus. Similar measurements with non-targeted bacteria show that the system is quite selective towards S. aureus. Our FL-based biosensor has a linear response in the range of 103-107 CFU mL-1 (colony formation unit mL-1) with a detection limit of 580 CFU mL-1. We have observed a fast response time of 15 minutes for sensing, which is superior to the previous reports. The proposed system was tested in human urine and can detect S. aureus in human urine samples selectively, proving its potential in real-life applications. The reported approach is versatile enough for sensing other biomolecules and metal ions by choosing suitable receptors.
Collapse
Affiliation(s)
- Abdul Kaium Mia
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, 781039, India.
| | - Abhilasha Bora
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, 781039, India.
| | - Md Tarik Hossain
- Department of Physics, Indian Institute of Technology Guwahati, 781039, India
| | - Swapnil Sinha
- IITG TIDF BioNEST, Indian Institute of Technology Guwahati, 781039, India
| | - P K Giri
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, 781039, India.
- Department of Physics, Indian Institute of Technology Guwahati, 781039, India
| |
Collapse
|