1
|
Zheng H, Munusamy S, Arora P, Jahani R, Guan X. A highly sensitive nanopore platform for measuring RNase A activity. Talanta 2024; 276:126276. [PMID: 38796995 PMCID: PMC11187776 DOI: 10.1016/j.talanta.2024.126276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024]
Abstract
Ribonuclease A (RNase A) plays significant roles in several physiological and pathological conditions and can be used as a valuable diagnostic biomarker for human diseases such as myocardial infarction and cancer. Hence, it is of great importance to develop a rapid and cost-effective method for the highly sensitive detection of RNase A. The significance of RNase A assay is further enhanced by the growing attention from the biotechnology and pharmaceutical industries to develop RNA-based vaccines and drugs in large part as a result of the successful development of mRNA vaccines in the COVID-19 pandemic. Herein, we report a label-free method for the detection of RNase A by monitoring its proteolytic cleavage of an RNA substrate in a nanopore. The method is ultra-sensitive with the limit of detection reaching as low as 30 fg per milliliter. Furthermore, sensor selectivity and the effects of temperature, incubation time, metal ion, salt concentration on sensor sensitivity were also investigated.
Collapse
Affiliation(s)
- Haiyan Zheng
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | | | - Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Rana Jahani
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA
| | - Xiyun Guan
- Department of Chemistry, University of Missouri, Columbia, MO 65211, USA.
| |
Collapse
|
2
|
Sikora H, Gruba N, Wysocka M, Piwkowska A, Lesner A. Optimization of fluorescent substrates for ADAM17 and their utility in the detection of diabetes. Anal Biochem 2023; 681:115337. [PMID: 37783443 DOI: 10.1016/j.ab.2023.115337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
ADAM17 (a disintegrin and metalloproteinase 17) is a sheddase that releases various types of membrane-associated proteins, including adhesive molecules, cytokines and their receptors, and inflammatory mediators. Evidence suggests that the enzyme is involved in the proteolytic cleavage of antiaging transmembrane protein Klotho (KL). What is more, reduced serum and urinary KL levels are observed in the early stages of chronic kidney disease. This study aimed to optimise the ADAM17 specific and selective fluorescent substrates. Then, the obtained substrate was used to detect the enzyme in urine samples of patients diagnosed with diabetes. It turned out that in all cases we were able to detect proteolytic activity, which was the opposite of the healthy samples.
Collapse
Affiliation(s)
- Honorata Sikora
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Natalia Gruba
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 Street, PL, 80-308, Gdańsk, Poland.
| | - Magdalena Wysocka
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Agnieszka Piwkowska
- Laboratory of Molecular and Cellular Nephrology, Mossakowski Medical Research Institute Polish Academy of Sciences, Wita Stwosza 63, 80-308, Gdansk, Poland; Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308, Gdansk, Poland
| | - Adam Lesner
- Department of Environmental Technology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 Street, PL, 80-308, Gdańsk, Poland
| |
Collapse
|
3
|
Zhang Y, Kim G, Zhu Y, Wang C, Zhu R, Lu X, Chang HC, Wang Y. Chiral Graphene Quantum Dots Enhanced Drug Loading into Small Extracellular Vesicles. ACS NANO 2023. [PMID: 37127891 DOI: 10.1021/acsnano.3c00305] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
As nanoscale extracellular vesicles secreted by cells, small extracellular vesicles (sEVs) have enormous potential as safe and effective vehicles to deliver drugs into lesion locations. Despite promising advances with sEV-based drug delivery systems, there are still challenges to drug loading into sEVs, which hinder the clinical applications of sEVs. Herein, we report an exogenous drug-agnostic chiral graphene quantum dots (GQDs) sEV-loading platform, based on chirality matching with the sEV lipid bilayer. Both hydrophobic and hydrophilic chemical and biological drugs can be functionalized or adsorbed onto GQDs by π-π stacking and van der Waals interactions. By tuning the ligands and GQD size to optimize its chirality, we demonstrate drug loading efficiency of 66.3% and 64.1% for doxorubicin and siRNA, which is significantly higher than other reported sEV loading techniques.
Collapse
Affiliation(s)
- Youwen Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Gaeun Kim
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yini Zhu
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Integrated Biomedical Sciences Graduate Program, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Runyao Zhu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Xin Lu
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| |
Collapse
|
4
|
Zhang Y, Zhu Y, Kim G, Wang C, Zhu R, Lu X, Chang HC, Wang Y. Chiral Graphene Quantum Dots Enhanced Drug Loading into Exosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.523510. [PMID: 36711460 PMCID: PMC9882333 DOI: 10.1101/2023.01.20.523510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As nanoscale extracellular vesicles secreted by cells, exosomes have enormous potential as safe and effective vehicles to deliver drugs into lesion locations. Despite promising advances with exosome-based drug delivery systems, there are still challenges to drug loading into exosome, which hinder the clinical applications of exosomes. Herein, we report an exogenous drug-agnostic chiral graphene quantum dots (GQDs) exosome-loading platform, based on chirality matching with the exosome lipid bilayer. Both hydrophobic and hydrophilic chemical and biological drugs can be functionalized or adsorbed onto GQDs by π-π stacking and van der Waals interactions. By tuning the ligands and GQD size to optimize its chirality, we demonstrate drug loading efficiency of 66.3% and 64.1% for Doxorubicin and siRNA, which is significantly higher than other reported exosome loading techniques.
Collapse
|
5
|
Chen X, Zhang Y, Guan X. Simultaneous detection of multiple proteases using a non-array nanopore platform. NANOSCALE 2021; 13:13658-13664. [PMID: 34477641 PMCID: PMC8485758 DOI: 10.1039/d1nr04085e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Multiplexing methods which are capable of measurement of multiple analytes in a single assay are of great importance in many fields. The conventional strategy for simultaneous detection of multiple species is to construct a sensor array. Herein, we report an innovative multiplex multi-analyte detection platform in a non-array format for protease measurement. By monitoring protease degradation of a single peptide substrate containing two cleavage sites for a disintegrin and metalloproteinase 10 (ADAM10) and a disintegrin and metalloproteinase 10 (ADAM17) in a single nanopore, simultaneous detection and quantification of these two model proteases in mixture samples could satisfactorily be accomplished. Our developed multiplexing sensing platform has the potential to be coupled with the traditional sensor array to further improve the multiplexing capability of the sensor, which may find useful applications in clinical diagnosis and prognosis.
Collapse
Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL 60616, USA.
| | | | | |
Collapse
|
6
|
Yao Y, Xie G, Zhang X, Yuan J, Hou Y, Chen H. Fast detection of E. coli with a novel fluorescent biosensor based on a FRET system between UCNPs and GO@Fe 3O 4 in urine specimens. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2209-2214. [PMID: 33908469 DOI: 10.1039/d1ay00320h] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biosensors based on nanomaterials are becoming a research hotspot for the rapid detection of pathogenic bacteria. Herein, a "turn-on" fluorescent biosensor based on a FRET system was constructed for the fast detection of a representative pathogenic microorganism, namely, E. coli, which causes most urinary tract infections. This biosensor was constructed by utilizing synthesized UCNPs as fluorescent donors with stable luminescence performance in complex biological samples and GO@Fe3O4 as a receptor with both excellent adsorption ability and fluorescence quenching ability. A specific ssDNA selected as an aptamer which could recognize E. coli was immobilized on the UCNPs to form UCNP-Apt nanoprobes. The nanoprobes were adsorbed on the surface of GO@Fe3O4 through the π-stacking interactions between aptamers and GO. In the presence of E. coli, UCNP-Apt nanoprobes detached from GO@Fe3O4 due to the specific recognition of aptamers and bacteria, resulting in obvious fluorescence recovery, and the concentration of bacteria was positively correlated with the intensity of the fluorescence signal; such a "turn-on" signal output mode ensures excellent precision. In addition, the easy magnetic separation of GO@Fe3O4 simplifies the operation process, helping the sensor detect bacteria in 30 minutes with a linear range from 103 to 107 CFU mL-1 and a limit of detection of 467 CFU mL-1. Moreover, recovery test results also showed that the sensor has clinical application potential for the rapid detection of pathogenic microorganisms in complex biological samples.
Collapse
Affiliation(s)
- Yuan Yao
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Xin Zhang
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Jinshan Yuan
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Yulei Hou
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| | - Hui Chen
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, P. R. China.
| |
Collapse
|
7
|
Zhang Y, Chen X, Yuan S, Wang L, Guan X. Joint Entropy-Assisted Graphene Oxide-Based Multiplexing Biosensing Platform for Simultaneous Detection of Multiple Proteases. Anal Chem 2020; 92:15042-15049. [PMID: 33118812 DOI: 10.1021/acs.analchem.0c03007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Due to the limited clinical utility of individual biomarkers, there is growing recognition of the need for combining multiple biomarkers as a panel to improve the accuracy and efficacy of disease diagnosis and prognosis. The conventional method to detect multiple analyte species is to construct a sensor array, which consists of an array of individual selective probes for different species. In this work, by using cancer biomarker matrix metalloproteinases (MMPs) and a disintegrin and metalloproteinases (ADAMs) as model analytes and functionalized nanographene oxide (nGO) as a sensing element, we developed a multiplexing fluorescence sensor in a nonarray format for simultaneous measurement of the activities of multiple proteases. The constructed nGO-based biosensor was rapid, sensitive, and selective and was also utilized for the successful profiling of ADAMs/MMPs in simulated serum samples. Furthermore, we showed that joint entropy and programming could be utilized to guide experiment design, especially in terms of the selection of a subset of proteases from the entire MMPs/ADAMs family as an appropriate biomarker panel. Our developed nGO-based multiplex sensing platform should find useful application in early cancer detection and diagnosis.
Collapse
Affiliation(s)
- Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Shaoqing Yuan
- Amazon, 2121 Seventh Avenue, Seattle, Washington 98121, United States
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China.,Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, Illinois 60616, United States
| |
Collapse
|
8
|
Qiang L, Zhang Y, Wu C, Han Y, Wang S, Wang Y, Zhang C, Liu G, Wu Q, Liu H, Jenkinson IR, Sun J, Han L. A Facile and Sensitive DNA Sensing of Harmful Algal Blooms Based on Graphene Oxide Nanosheets. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:498-510. [PMID: 32358654 DOI: 10.1007/s10126-020-09971-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 04/08/2020] [Indexed: 06/11/2023]
Abstract
Gene detection has important applications in biology, biomedical engineering, clinical, environmental, and marine fields. Rapid, sensitive, and selective recognition of specific genes is essential in practical applications. In this study, we describe a facile and sensitive DNA sensing platform for specific and quantitative detection of Heterosigma akashiwo, which is one of the causative agents of red tides. Fast and sensitive detection is achieved by using chemically synthesized graphene oxide (GO) nanosheets. Probe DNA is designed according to the specific DNA fragments of harmful algae and labeled with fluorescent molecules FAM (fluorescein-based dye). GO nanosheet solution is made, in which the strong interaction between FAM-labeled probe and GO nanosheets keeps them in close proximity, facilitating the fluorescence quenching of the fluorophore by GO nanosheets. In the presence of a complementary target DNA, the FAM-labeled DNA probe and the target DNA hybridize and desorb from the surface of GO nanosheets, resulting in restoration of fluorophore fluorescence. The concentration of target DNA fragments is analyzed by the fluorescence intensity at ~ 520 nm with emission wavelength of 480 nm. The sensitive detecting platform achieved stable measurement of 1 pM specific genes from Heterosigma akashiwo. Our GO nanosheet-based DNA-sensing platform performs fast and sensitive detection of trace amount of DNA, and enables quantitative recognition of harmful algae, which has promising applications in real-time monitoring in the marine environment of red tide generative dynamics, allowing effective control, particularly in relation to marine aquaculture.
Collapse
Affiliation(s)
- Le Qiang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Yu Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| | - Chao Wu
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Yingkuan Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
- School of Microelectronics, Shandong University, Jinan, 250010, China
| | - Suchun Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Yanyan Wang
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Congcong Zhang
- Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan, 250022, China
| | - Guangzhou Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Qi Wu
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China
| | - Hong Liu
- Institute for Advanced Interdisciplinary Research (iAIR), University of Jinan, Jinan, 250022, China
- State Key Laboratory of Crystal Materials, Center of Bio & Micro/Nano Functional Materials, Shandong University, Jinan, 250100, Shandong, China
| | - Ian R Jenkinson
- Agency for Consultation and Research in Oceanography, 19320, La Roche Canillac, France
| | - Jun Sun
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
- Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Lin Han
- Institute of Marine Science and Technology, Shandong University, Qingdao, 266237, China.
| |
Collapse
|
9
|
Two-Channel Graphene pH Sensor Using Semi-Ionic Fluorinated Graphene Reference Electrode. SENSORS 2020; 20:s20154184. [PMID: 32731474 PMCID: PMC7436108 DOI: 10.3390/s20154184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/16/2020] [Accepted: 07/27/2020] [Indexed: 02/05/2023]
Abstract
A reference electrode is necessary for the working of ion-sensitive field-effect transistor (ISFET)-type sensors in electrolyte solutions. The Ag/AgCl electrode is normally used as a reference electrode. However, the Ag/AgCl reference electrode limits the advantages of the ISFET sensor. In this work, we fabricated a two-channel graphene solution gate field-effect transistor (G-SGFET) to detect pH without an Ag/AgCl reference electrode in the electrolyte solution. One channel is the sensing channel for detecting the pH and the other channel is the reference channel that serves as the reference electrode. The sensing channel was oxygenated, and the reference channel was fluorinated partially. Both the channels were directly exposed to the electrolyte solution without sensing membranes or passivation layers. The transfer characteristics of the two-channel G-SGFET showed ambipolar field-effect transistor (FET) behavior (p-channel and n-channel), which is a typical characteristic curve for the graphene ISFET, and the value of VDirac was shifted by 18.2 mV/pH in the positive direction over the range of pH values from 4 to 10. The leakage current of the reference channel was 16.48 nA. We detected the real-time pH value for the two-channel G-SGFET, which operated stably for 60 min in the buffer solution.
Collapse
|
10
|
Zhang Y, Chen X, Wang C, Roozbahani GM, Chang HC, Guan X. Chemically functionalized conical PET nanopore for protein detection at the single-molecule level. Biosens Bioelectron 2020; 165:112289. [PMID: 32729470 DOI: 10.1016/j.bios.2020.112289] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 12/18/2022]
Abstract
Proteins are essential for all living organisms, and perform a wide variety of functions in the cell and human body, including structural, mechanical, biochemical, and signaling. Since proteins can serve as valuable biomarkers for health status and diseases states, and enable personalized medicine, sensitive and rapid detection of proteins is of paramount importance. Herein, we report a chemically functionalized conical shaped poly-(ethylene terephthalate) nanopore (PET nanopore) as a stochastic sensing element for detection of proteins at the single-molecule level. We demonstrate that the PET nanopore sensor is not only sensitive and selective, but also can differentiate proteins rapidly, offering the potential for label-free protein detection and characterization. Our developed PET nanopore sensing strategy not only provides a general platform for exploring fundamental protein dynamics and rapid detection of proteins at the single-molecule level, but also opens new avenues toward advanced deeper understanding of enzymes, development of more efficient biosensing technologies, and constructing novel biomimetic nanopore systems.
Collapse
Affiliation(s)
- Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA.
| |
Collapse
|
11
|
Roozbahani GM, Zhang Y, Chen X, Soflaee MH, Guan X. Enzymatic reaction-based nanopore detection of zinc ions. Analyst 2019; 144:7432-7436. [PMID: 31691699 DOI: 10.1039/c9an01784d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a label-free nanopore sensor for the detection of Zn2+ ions. By taking advantage of the cleavage of a substrate peptide by zinc-dependent enzymes, nanomolar concentrations of Zn2+ ions could be detected within minutes. Furthermore, structurally similar transition metals such as Ni2+, Co2+, Hg2+, Cu2+, and Cd2+ did not interfere with their detection. The enzymatic reaction-based nanopore sensing strategy developed in this work may find potential applications in environmental monitoring and medical diagnosis.
Collapse
|