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Wang R, Zhang Y, Ma QDY, Wu L. Recent advances of small molecule detection in nanopore sensing. Talanta 2024; 277:126323. [PMID: 38810384 DOI: 10.1016/j.talanta.2024.126323] [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: 03/15/2024] [Revised: 05/04/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
Due to its advantages of label-free and highly sensitive, the resistive pulse sensing with a nanopore has recently become even more potent for the discrimination of analytes in single molecule level. Generally, a transient interruption of ion current originated from the captured molecule passing through a nanopore will provide the rich information on the structure, charge and translocation dynamics of the analytes. Therefore, nanopore sensors have been widely used in the fields of DNA sequencing, protein recognition, and the portable detection of varied macromolecules and particles. However, the conventional nanopore devices are still lack of sufficient selectivity and sensitivity to distinguish more metabolic molecules involving ATP, glucose, amino acids and small molecular drugs because it is hard to receive a large number of identifiable signals with the fabricated pores comparable in size to small molecules for nanopore sensing. For all this, a series of innovative strategies developed in the past decades have been summarized in this review, including host-guest recognition, engineering alteration of protein channel, the introduction of nucleic acid aptamers and various delivery carriers integrating signal amplification sections based on the biological and solid nanopore platforms, to achieve the high resolution for the small molecules sensing in micro-nano environment. These works have greatly enhanced the powerful sensing capabilities and extended the potential application of nanopore sensors.
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Affiliation(s)
- Runyu Wang
- College of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Yinuo Zhang
- College of Integrated Circuit Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China
| | - Qianli D Y Ma
- College of Integrated Circuit Science and Engineering, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China.
| | - Lingzhi Wu
- College of Science, Nanjing University of Posts and Telecommunications, Nanjing, 210046, China.
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de la Torre M, Pomorski A. Investigation of metal ion binding biomolecules one molecule at a time. Front Chem 2024; 12:1378447. [PMID: 38680456 PMCID: PMC11045889 DOI: 10.3389/fchem.2024.1378447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/22/2024] [Indexed: 05/01/2024] Open
Abstract
Metal ions can perform multiple roles ranging from regulatory to structural and are crucial for cell function. While some metal ions like Na+ are ubiquitously present at high concentrations, other ions, especially Ca2+ and transition metals, such as Zn2+ or Cu+/2+ are regulated. The concentrations above or below the physiological range cause severe changes in the behavior of biomolecules that bind them and subsequently affect the cell wellbeing. This has led to the development of specialized protocols to study metal ion binding biomolecules in bulk conditions that mimic the cell environment. Recently, there is growing evidence of influence of post-transcriptional and post-translational modifications on the affinity of the metal ion binding sites. However, such targets are difficult to obtain in amounts required for classical biophysical experiments. Single molecule techniques have revolutionized the field of biophysics, molecular and structural biology. Their biggest advantage is the ability to observe each molecule's interaction independently, without the need for synchronization. An additional benefit is its extremely low sample consumption. This feature allows characterization of designer biomolecules or targets obtained coming from natural sources. All types of biomolecules, including proteins, DNA and RNA were characterized using single molecule methods. However, one group is underrepresented in those studies. These are the metal ion binding biomolecules. Single molecule experiments often require separate optimization, due to extremely different concentrations used during the experiments. In this review we focus on single molecule methods, such as single molecule FRET, nanopores and optical tweezers that are used to study metal ion binding biomolecules. We summarize various examples of recently characterized targets and reported experimental conditions. Finally, we discuss the potential promises and pitfalls of single molecule characterization on metal ion binding biomolecules.
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Affiliation(s)
| | - Adam Pomorski
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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Electrochemical Biosensor Using Nitrogen-Doped Graphene/Au Nanoparticles/DNAzyme for Ca2+ Determination. BIOSENSORS 2022; 12:bios12050331. [PMID: 35624632 PMCID: PMC9138538 DOI: 10.3390/bios12050331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 12/16/2022]
Abstract
An electrochemical biosensor for detecting Ca2+ concentration was proposed using glass carbon electrodes (GCEs) modified with nitrogen-doped graphene (NGR), gold nanoparticles (AuNPs) and DNAzyme. The resistance signal was amplified through two methods: electrochemical reduction of AuNPs on the NGR surface to increase the specific surface area of the electrode and strengthen the adsorption of DNAzyme; and increasement of the DNAzyme base sequence. The process of electrode modification was characterized by scanning electron microscopy, Raman spectroscopy, cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS). Experimental parameters’ influence, such as the deposition time of gold nanoparticles and the detection time, were assessed by electrochemical methods. The linear ranges of the electrochemical biosensor were in the range from 5 × 10−6 to 5 × 10−5 and 5 × 10−5 to 4 × 10−4 M, with a detection limit of 3.8 × 10−6 M. The concentration of Ca2+ in the serum of dairy cows was determined by the biosensor with satisfactory results, which could be potentially used to diagnose subclinical hypocalcemia.
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Wang H, Luo Q, Zhao Y, Nan X, Zhang F, Wang Y, Wang Y, Hua D, Zheng S, Jiang L, Yang L, Xiong B. Electrochemical device based on nonspecific DNAzyme for the high-accuracy determination of Ca 2+ with Pb 2+ interference. Bioelectrochemistry 2020; 140:107732. [PMID: 33465700 DOI: 10.1016/j.bioelechem.2020.107732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Calcium is one of the most abundant and indispensable elements in biology, as it is a vital component of nerves, bones, and muscles and maintains the excitability of normal neuromuscular muscles. However, it may be harmful to the human body and even damage the organs if the calcium content exceeds the standard value by several times. To evaluate the level of calcium ions (Ca2+), an electrochemical biosensor (FET/SWNTs/Cazyme) was developed using a nonspecific DNAzyme with high stability, which combined the unique advantage of field-effect transistors and single-walled carbon nanotubes, while being easy-to-use and having excellent sensitivity. The incubation time and voltage after optimization were 15 min and +0.02 V. The nonspecific DNAzyme-based biosensor was sensitive to Ca2+, but it was also interfered with by Pb2+, which affected the detection accuracy. To solve this shortcoming, an electrochemical device was proposed, in which FET/SWNTs/Cazyme combined with other specific biosensors for Pb2+, and then established some data processing models were established through support vector machine regression (SVMR) and artificial neural network fitting (ANNF). For the optimal SVMR, the electrochemical device can determine the Ca2+ concentration in the range of 7.5-1000 μM with a detection limit of 5.48 μM. Finally, the prepared electrochemical device was employed to detect the Ca2+ in different milk and water samples.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Qingyao Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yiguang Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xuemei Nan
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Fan Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, PR China
| | - Yaping Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Yue Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China; College of Animal Science and Technology, Northwest A&F University, Yangling 712100, PR China
| | - Dengke Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Shanshan Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Linshu Jiang
- School of Animal Science and Technology, Beijing Agricultural University, Beijing Key Laboratory of Dairy Nutrition, Beijing 102206, PR China
| | - Liang Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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