330 results on '"Yi-Tao Long"'
Search Results
2. Direct Quantification of Damaged Nucleotides in Oligonucleotides Using an Aerolysin Single Molecule Interface
- Author
-
Jiajun Wang, Meng-Yin Li, Jie Yang, Ya-Qian Wang, Xue-Yuan Wu, Jin Huang, Yi-Lun Ying, and Yi-Tao Long
- Subjects
Chemistry ,QD1-999 - Published
- 2020
- Full Text
- View/download PDF
3. Simultaneous Removal of Multiple Heavy Metal Ions from River Water Using Ultrafine Mesoporous Magnetite Nanoparticles
- Author
-
Fato Patrice Fato, Da-Wei Li, Li-Jun Zhao, Kaipei Qiu, and Yi-Tao Long
- Subjects
Chemistry ,QD1-999 - Published
- 2019
- Full Text
- View/download PDF
4. pH-Dependent Water Clusters in Photoacid Solution: Real-Time Observation by ToF-SIMS at a Submicropore Confined Liquid-Vacuum Interface
- Author
-
Ying-Ya Liu, Xin Hua, Zhiwei Zhang, Junji Zhang, Shaoze Zhang, Ping Hu, and Yi-Tao Long
- Subjects
in-situ liquid ToF-SIMS ,liquid-vacuum interface ,photoacid ,water cluster ,hydrogen-bonding network ,Chemistry ,QD1-999 - Abstract
Water clusters are ubiquitously formed in aqueous solutions by hydrogen bonding, which is quite sensitive to various environment factors such as temperature, pressure, electrolytes, and pH. Investigation of how the environment has impact on water structure is important for further understanding of the nature of water and the interactions between water and solutes. In this work, pH-dependent water structure changes were studied by monitoring the changes for the size distribution of protonated water clusters by in-situ liquid ToF-SIMS. In combination with a light illumination system, in-situ liquid ToF-SIMS was used to real-time measure the changes of a light-activated organic photoacid under different light illumination conditions. Thus, the proton transfer and pH-mediated water cluster changes were analyzed in real-time. It was found that higher concentration of free protons could lead to a strengthened local hydrogen bonding network as well as relatively larger protonated water clusters in both organic acid and inorganic acid. Besides, the accumulation of protons at the liquid-vacuum interface under light illumination was observed owing to the affinity of organic molecules to the low-pressure gas phase. The application of in-situ liquid ToF-SIMS analysis in combination with in-situ light illumination system opened up an avenue to real-time investigate light-activated reactions. Besides, the results regarding water structure changes in acidic solutions showed important insights in related atmospheric and physiochemical processes.
- Published
- 2020
- Full Text
- View/download PDF
5. Single Molecule Study of Hydrogen Bond Interactions Between Single Oligonucleotide and Aerolysin Sensing Interface
- Author
-
Meng-Yin Li, Ya-Qian Wang, Yao Lu, Yi-Lun Ying, and Yi-Tao Long
- Subjects
single-molecule interface ,oligonucleotide ,nanopore ,hydrogen bond ,nanoconfinement ,Chemistry ,QD1-999 - Abstract
The aerolysin nanopore displays a charming sensing capability for single oligonucleotide discrimination. When reading from the electrochemical signal, stronger interaction between the aerolysin nanopore and oligonucleotide represent prolonged duration time, thereby amplifying the hidden but intrinsic signal thus improving the sensitivity. In order to further understand and optimize the performance of the aerolysin nanopore, we focus on the investigation of the hydrogen bond interaction between nanopore, and analytes. Taking advantage of site-direct mutagenesis, single residue is replaced. According to whole protein sequence screening, the region near K238 is one of the key sensing regions. Such a positively charged amino acid is then mutagenized into cysteine and tyrosine denoted as K238C, and K238Y. As (dA)4 traverses the pores, K238C dramatically produces a six times longer duration time than the WT aerolysin nanopore at the voltage of +120 mV. However, K238Y shortens the dwell time which suggests the acceleration of the translocation causing poor sensitivity. Referring to our previous findings in K238G, and K238F, our results suggest that the hydrogen bond does not dominate the dynamic translocation process, but enhances the interaction between pores and analytes confined in such nanopore space. These insights give detailed information for the rational design of the sensing mechanism of the aerolysin nanopore, thereby providing further understanding for the weak interactions between biomolecules and the confined space for nanopore sensing.
- Published
- 2019
- Full Text
- View/download PDF
6. Nanopore-based measurement of the interaction of P450cam monooxygenase and putidaredoxin at the single-molecule level
- Author
-
Shelley D. Minteer, Yao Lin, Hui Chen, Yi-Lun Ying, and Yi-Tao Long
- Subjects
Range (particle radiation) ,Camphor 5-Monooxygenase ,Chemistry ,Ionic bonding ,Monooxygenase ,Redox ,Mixed Function Oxygenases ,Characterization (materials science) ,Electron Transport ,Nanopores ,Nanopore ,Chemical physics ,Ferredoxins ,Molecule ,Physical and Theoretical Chemistry ,Nanoscopic scale - Abstract
Protein-protein interactions occur in a wide range of biological processes and are of great significance to life function. Characterization of transient protein-protein interactions remains a significant barrier to our understanding of cellular processes. Nanopores provide unique nanoscale environments that accommodate single molecules from the surrounding bulk solution. This method permits label-free sensing at the single-molecule level with extremely high sensitivity. Herein, the interaction between a single P450cam monooxygenase and its redox partner putidaredoxin (Pdx) was monitored via transient ionic current by using functionalized glass nanopores. Results show that the volume of P450cam determines the blockage current while the interactions between the P450cam and Pdx give a long blockage duration. Our glass nanopore sensor with adjustable diameter could be applied for real-time sensing of protein-protein interactions between individual proteins with a wide range of molecular weight.
- Published
- 2022
7. Is the Volume Exclusion Model Practicable for Nanopore Protein Sequencing?
- Author
-
Meng-Yin Li, Yi-Lun Ying, Yi-Tao Long, and Ming-Zhu Huo
- Subjects
Nanopores ,Nanopore ,Protein sequencing ,Sequence Analysis, Protein ,Chemistry ,Biophysics ,Proteins ,Amino Acid Sequence ,Peptides ,Analytical Chemistry - Abstract
The nanopore approach holds the possibility for achieving single-molecule protein sequencing. However, ongoing challenges still remain in the biological nanopore technology, which aims to identify 20 natural amino acids by reading the ionic current difference with the traditional current-sensing model. In this paper, taking aerolysin nanopores as an example, we calculate and compare the current blockage of each of 20 natural amino acids, which are all far from producing a detectable current blockage difference. Then, we propose a modified solution conductivity of σ' in the traditional volume exclusion model for nanopore sensing of a peptide. The σ' value describes the comprehensive result of ion mobility inside a nanopore, which is related to but not limited to nanopore-peptide interactions, and the positions, orientations, and conformations of peptides inside the nanopore. The nanopore experiments of a short peptide (VQIVYK) in wild type and mutant nanopores further demonstrate that the traditional volume exclusion model is not enough to fully explain the current blockage contribution and that many other factors such as enhanced nanopore-peptide interactions could contribute to a dominant part of the current change. This modified sensing model provides insights into the further development of nanopore protein sequencing methods.
- Published
- 2021
8. Understanding the Dynamic Potential Distribution at the Electrode Interface by Stochastic Collision Electrochemistry
- Author
-
Jianfu Chen, Yi-Tao Long, Hui Ma, Yue-Yi Peng, Haifeng Wang, Wei Ma, Peijun Hu, and Si-Min Lu
- Subjects
Distribution (number theory) ,Chemistry ,Nanoparticle ,General Chemistry ,Electrode interface ,Electrochemistry ,Collision ,Biochemistry ,Catalysis ,Colloid and Surface Chemistry ,Chemical physics ,Electrode ,Nanoscopic scale ,Electrode potential - Abstract
The potential distribution at the electrode interface is a core factor in electrochemistry, and it is usually treated by the classic Gouy-Chapman-Stern (G-C-S) model. Yet the G-C-S model is not applicable to nanosized particles collision electrochemistry as it describes steady-state electrode potential distribution. Additionally, the effect of single nanoparticles (NPs) on potential should not be neglected because the size of a NP is comparable to that of an electrode. Herein, a theoretical model termed as Metal-Solution-Metal Nanoparticle (M-S-MNP) is proposed to reveal the dynamic electrode potential distribution at the single-nanoparticle level. An explicit equation is provided to describe the size/distance-dependent potential distribution in single NPs stochastic collision electrochemistry, showing the potential distribution is influenced by the NPs. Agreement between experiments and simulations indicates the potential roles of the M-S-MNP model in understanding the charge transfer process at the nanoscale.
- Published
- 2021
9. An Envelope Algorithm for Single Nanoparticle Collision Electrochemistry †
- Author
-
Chun-Yu Xu, Yong-Jing Wan, Ru-Jia Yu, Yi-Tao Long, Xi-Xin Fu, Su-Wen Xu, Xue Ni, and Yi-Lun Ying
- Subjects
Savitzky–Golay filter ,Chemistry ,Nanoparticle ,General Chemistry ,Electrochemistry ,Collision ,Molecular physics ,Envelope (waves) - Published
- 2021
10. Biological Nanopore Approach for Single‐Molecule Protein Sequencing
- Author
-
Yi-Tao Long, Yi-Lun Ying, Ming-Zhu Huo, and Zheng-Li Hu
- Subjects
Models, Molecular ,chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Proteins ,Peptide ,General Medicine ,General Chemistry ,Computational biology ,010402 general chemistry ,Proteomics ,01 natural sciences ,Catalysis ,DNA sequencing ,0104 chemical sciences ,Amino acid ,Nanopores ,Nanopore ,Protein sequencing ,Sequence Analysis, Protein ,Native protein ,Molecule - Abstract
Proteins are responsible for the occurrence and treatment of many diseases, and therefore protein sequencing will revolutionize proteomics and clinical diagnostics. Biological nanopore approach has proved successful for single-molecule DNA sequencing, which resolves the identities of 4 natural deoxyribonucleotides based on the current blockages and duration times of their translocations across the nanopore confinement. However, open challenges still remain for biological nanopores to sequentially identify each amino acid (AA) of single proteins due to the inherent complexity of 20 proteinogenic AAs in charges, volumes, hydrophobicity and structures. Herein, we focus on recent exciting advances in biological nanopores for single-molecule protein sequencing (SMPS) from native protein unfolding, control of peptide translocation, AA identification to applications in disease detection.
- Published
- 2021
11. Unveiling the Heterogenous Dephosphorylation of DNA Using an Aerolysin Nanopore
- Author
-
Ya-Qian Wang, Xue-Yuan Wu, Yi-Lun Ying, Yi-Tao Long, Shuang Li, and Meng-Yin Li
- Subjects
Pore Forming Cytotoxic Proteins ,Kinase ,Bacterial Toxins ,Phosphatase ,General Engineering ,Aerolysin ,General Physics and Astronomy ,DNA ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Cell biology ,Dephosphorylation ,Nanopores ,chemistry.chemical_compound ,chemistry ,Phosphorylation ,Alkaline phosphatase ,General Materials Science ,0210 nano-technology ,Fetal bovine serum - Abstract
The simultaneous occurrence of multiple heterogeneous DNA phosphorylation statuses, which include 5' end phosphorylation, 5' end dephosphorylation, 3' end phosphorylation, and 3' end dephosphorylation, is crucial for regulating numerous cellular processes. Although there are many methods for detecting a single type of DNA phosphorylation, the direct and simultaneous identification of DNA phosphorylation/dephosphorylation on the 5' and/or 3' ends remains a challenge, let alone the unveiling of the heterogeneous catalysis processes of related phosphatases and kinases. Taking advantage of the charge-sensitive aerolysin nanopore interface, herein, an orientation-dependent sensing strategy is developed to enhance phosphorylation-site-dependent interaction with the nanopore sensing interface, enabling the direct and simultaneous electric identification of four heterogeneous phosphorylation statuses of a single DNA. By using this strategy, we can directly evaluate the heterogeneous dephosphorylation process of alkaline phosphatase (ALP) at the single-molecule level. Our results demonstrate that the ALP in fetal bovine serum preferentially catalyzes the 3' phosphate rather than both ends. The quantification of endogenous ALP activity in fetal bovine serum could reach the submilli-IU/L level. Our aerolysin measurements provide a direct look at the heterogeneous phosphorylation status of DNA, allowing the unveiling of the dynamic single-molecule functions of kinase and phosphatase.
- Published
- 2020
12. Direct Quantification of Damaged Nucleotides in Oligonucleotides Using an Aerolysin Single Molecule Interface
- Author
-
Yi-Tao Long, Yi-Lun Ying, Jiajun Wang, Jie Yang, Xue-Yuan Wu, Ya-Qian Wang, Meng-Yin Li, and Jin Huang
- Subjects
chemistry.chemical_classification ,010405 organic chemistry ,Chemistry ,Oligonucleotide ,General Chemical Engineering ,Mutant ,Aerolysin ,General Chemistry ,010402 general chemistry ,01 natural sciences ,DNA sequencing ,0104 chemical sciences ,Lesion ,Nanopore ,chemistry.chemical_compound ,Biophysics ,medicine ,Nucleotide ,medicine.symptom ,QD1-999 ,DNA ,Research Article - Abstract
DNA lesions such as metholcytosine(mC), 8-OXO-guanine (OG), inosine (I), etc. could cause genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remains a challenge due to massive varieties and less distinguishable readouts for structural variations at the molecular level. Moreover, standard amplification and labeling hardly work in DNA lesion detection. Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor lesion into distinguishable electrochemical readouts. Compared with previous single molecule sensing interfaces, the temporal resolution of the K238Q aerolysin nanopore is enhanced by two orders, which has the best sensing performance in all reported aerolysin nanopores. In this work, the novel K238Q could discriminate directly at least three types of lesions (mC, OG, I) without labeling and quantify modification sites under the mixed heterocomposition conditions of the oligonucleotide. Such a nanopore electrochemistry approach could be further applied to diagnose genetic diseases at high sensitivity., Herein, we designed a single molecule interface from the mutant aerolysin (K238Q), whose sensing region shows high compatibility to capture and then directly convert a minor DnA lesion into distinguishable electrochemical readouts.
- Published
- 2020
13. The analysis of single cysteine molecules with an aerolysin nanopore
- Author
-
Bo Yuan, Yi-Tao Long, Yi-Lun Ying, and Shuang Li
- Subjects
Models, Molecular ,Pore Forming Cytotoxic Proteins ,Protein Conformation ,Bacterial Toxins ,Lipid Bilayers ,Aerolysin ,Biosensing Techniques ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Analytical Chemistry ,Nanopores ,Protein structure ,Protein sequencing ,Limit of Detection ,Electrochemistry ,Environmental Chemistry ,Molecule ,Cysteine ,Spectroscopy ,chemistry.chemical_classification ,Biomolecule ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Amino acid ,Nanopore ,chemistry ,Biophysics ,0210 nano-technology - Abstract
Biological nanopore technology has the advantages of high selectivity and high reproducibility for characterizing single biomolecules. However, it is challenging to achieve protein sequencing owing to the heterogeneous charge distributions of the protein and the small structural difference from each amino acid. Here, we took the inherent electrochemically confined sensing interface of the aerolysin nanopore to enhance its interaction with single amino acids. The results showed that single cysteine molecules, a highly reactive amino acid in aging and neurodegenerative diseases, could be captured and monitored by an aerolysin nanopore as it produced distinctive current blockages with a prolonged statistical duration of 0.11 ± 0.02 ms at +120 mV. This is the first report of the detection of a single amino acid molecule by a biological nanopore directly without any modification and labelling. This study facilitates the direct detection of single amino acids by regulating the characteristic interaction between the single amino acids and the designed sensing interface of aerolysin nanopores.
- Published
- 2020
14. The Effects of Tetramethylammonium Cation on Oligonucleotide Analysis with Aerolysin Nanopore
- Author
-
Yi-Lun Ying, Meng-Yin Li, Yi-Tao Long, and Xue-Yuan Wu
- Subjects
Tetramethylammonium ,Nanopore ,chemistry.chemical_compound ,chemistry ,Oligonucleotide ,Electrochemistry ,Aerolysin ,Combinatorial chemistry ,Catalysis - Published
- 2019
15. Single molecule sensing of amyloid-β aggregation by confined glass nanopores† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c9sc03260f
- Author
-
Su-Wen Xu, Ru-Jia Yu, Si-Min Lu, Yi-Lun Ying, Yuan-Jie Li, Qun Xu, and Yi-Tao Long
- Subjects
Amyloid β ,Amyloid ,010405 organic chemistry ,Chemistry ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Oligomer ,0104 chemical sciences ,chemistry.chemical_compound ,Nanopore ,Adsorption ,Molecular size ,Biophysics ,Molecule ,Surface charge - Abstract
We have employed glass nanopore as a single molecule technique for direct sensing amyloidosis process of Aβ1–42 peptide, which of great significance in Alzheimer's disease., We have developed a glass nanopore based single molecule tool to investigate the dynamic oligomerization and aggregation process of Aβ1–42 peptides. The intrinsic differences in the molecular size and surface charge of amyloid aggregated states could be distinguished through single molecule induced characteristic current fluctuation. More importantly, our results reveal that the neurotoxic Aβ1–42 oligomer tends to adsorb onto the solid surface of nanopores, which may explain its instability and highly neurotoxic features.
- Published
- 2019
16. Enhanced identification of Tau acetylation and phosphorylation with an engineered aerolysin nanopore
- Author
-
Zheng-Li Hu, Yi-Tao Long, Ming-Zhu Huo, and Yi-Lun Ying
- Subjects
Pore Forming Cytotoxic Proteins ,Protein function ,Chemistry ,Lysine ,Bacterial Toxins ,Aerolysin ,Acetylation ,tau Proteins ,Protein Engineering ,Biochemistry ,Nanopore ,Nanopores ,Tau phosphorylation ,Biophysics ,Phosphorylation ,Threonine ,Molecular Biology ,Protein Processing, Post-Translational - Abstract
Posttranslational modifications (PTMs) affect protein function/dysfunction, playing important roles in the occurrence and development of tauopathies including Alzheimer's disease. PTM detection is significant and still challenging due to the requirements of high sensitivity to identify the subtle structural differences between modifications. Herein, in terms of the unique geometry of the aerolysin (AeL) nanopore, we elaborately engineered a T232K AeL nanopore to detect the acetylation and phosphorylation of Tau segment (Pep). By replacing neutral threonine (T) with positively charged lysine (K) at the 232 sites, the T232K and K238 rings of this engineered T232K AeL nanopore corporately work together to enhance electrostatic trapping of the acetylated and phosphorylated Tau peptides. Translocation speed of the monophosphorylated Pep-P was decelerated by up to 46 folds compared to the wild-type (WT) AeL nanopore. The prolonged residences within the T232K AeL nanopore enabled to simultaneously identify the monoacetylated Pep-Ac, monophosphorylated Pep-P, di-modified Pep-P-Ac and non-modified Pep. The tremendous potential is demonstrated for PTM sensing by manipulating non-covalent interactions between nanopores and single analytes.
- Published
- 2021
17. Snapshotting the transient conformations and tracing the multiple pathways of single peptide folding using a solid-state nanopore
- Author
-
Weihua Li, Yong-Jing Wan, Yi-Lun Ying, Yi-Tao Long, and Shao-Chuang Liu
- Subjects
chemistry.chemical_classification ,Time evolution ,Non-equilibrium thermodynamics ,Peptide ,02 engineering and technology ,General Chemistry ,Tracing ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Folding (chemistry) ,Nanopore ,Chemistry ,chemistry ,Biophysics ,Protein folding ,Transient (oscillation) ,0210 nano-technology - Abstract
A fundamental question relating to protein folding/unfolding is the time evolution of the folding of a protein into its precisely defined native structure. The proper identification of transition conformations is essential for accurately describing the dynamic protein folding/unfolding pathways. Owing to the rapid transitions and sub-nm conformation differences involved, the acquisition of the transient conformations and dynamics of proteins is difficult due to limited instrumental resolution. Using the electrochemical confinement effect of a solid-state nanopore, we were able to snapshot the transient conformations and trace the multiple transition pathways of a single peptide inside a nanopore. By combining the results with a Markov chain model, this new single-molecule technique is applied to clarify the transition pathways of the β-hairpin peptide, which shows nonequilibrium fluctuations among several blockage current stages. This method enables the high-throughput investigation of transition pathways experimentally to access previously obscure peptide dynamics, which is significant for understanding the folding/unfolding mechanisms and misfolding of peptides or proteins., A solid-state nanopore based method is described for resolving protein-folding-related problems via snapshotting the folding intermediates and characterizing the kinetics of a single peptide.
- Published
- 2021
18. Tracking the Electrocatalytic Activity of a Single Palladium Nanoparticle for the Hydrogen Evolution Reaction
- Author
-
Zhifeng Ding, Yue-Yi Peng, Si-Min Lu, Yi-Tao Long, and Mengjie Chen
- Subjects
Chemistry ,Organic Chemistry ,Palladium nanoparticles ,chemistry.chemical_element ,Nanoparticle ,Metal Nanoparticles ,Nanotechnology ,General Chemistry ,Electrochemistry ,Tracking (particle physics) ,Catalysis ,Electrode ,Hydrogen evolution ,Electrodes ,Palladium ,Hydrogen - Abstract
The nanoparticle-based electrocatalysts' performance is directly related to their working conditions. In general, a number of nanoparticles are uncontrollably fixed on a millimetre-sized electrode for electrochemical measurements. However, it is hard to reveal the maximum electrocatalytic activity owing to the aggregation and detachment of nanoparticles on the electrode surface. To solve this problem, here, we take the hydrogen evolution reaction (HER) catalyzed by palladium nanoparticles (Pd NPs) as a model system to track the electrocatalytic activity of single Pd NPs by stochastic collision electrochemistry and ensemble electrochemistry, respectively. Compared with the nanoparticle fixed working condition, Pd NPs in the nanoparticle diffused working condition results in a 2-5 orders magnitude enhancement of electrocatalytic activity for HER at various bias potential. Stochastic collision electrochemistry with high temporal resolution gives further insights into the accurate study of NPs' electrocatalytic performance, enabling to dramatically enhance electrocatalytic efficiency.
- Published
- 2021
19. Ion-Specific Effects on Hydrogen Bond Network at a Submicropore Confined Liquid-Vacuum Interface: An in Situ Liquid ToF-SIMS Study
- Author
-
Hai-Lun Xia, Xin Hua, Ying-Ya Liu, Yi-Tao Long, Yi-Lun Ying, and Shao-Ze Zhang
- Subjects
In situ ,Properties of water ,Materials science ,Hydrogen bond ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Ion ,chemistry.chemical_compound ,chemistry ,Chemical physics ,Molecule ,General Materials Science ,Physical and Theoretical Chemistry ,0210 nano-technology - Abstract
The hydrogen bond (HB), one of the essential properties of water, tends to link water molecules to form dynamic water clusters. Extrinsic ions could change the size distribution of water clusters b...
- Published
- 2019
20. Monitoring Hydrogen Evolution Reaction Catalyzed by MoS2 Quantum Dots on a Single Nanoparticle Electrode
- Author
-
Yan Wang, Yi-Lun Ying, Jian-Fang Zhang, Yi-Tao Long, Yuan-Jie Li, and Si-Min Lu
- Subjects
Nanocomposite ,Chemistry ,010401 analytical chemistry ,Nanoparticle ,Ionic bonding ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Catalysis ,Nanopore ,Chemical engineering ,Quantum dot ,Electrode ,Particle - Abstract
Hydrogen evolution reaction (HER) catalyzed by molybdenum sulfide quantum dots (MoS2 QDs) has attracted extensive attention in the energy field. Monitoring HER catalyzed by MoS2 QDs based on a glass nanopore with an electrochemically confined effect was proposed for the first time. MoS2 QDs inside the glass nanopore is driven toward the orifice of the nanopore and bonded with the Ag nanoparticles (Ag NPs) to form a single nanocomposite. When enough voltage is applied across the orifice, the single Ag NP acts as a single nanoparticle electrode to conduct the electrochemically bipolar reaction on its two extremities. In the process, HER is catalyzed by MoS2 QDs, and Ag NPs are oxidized at the same time. The appearance of blockages on the elevated ionic current is attributed to the generation of a H2 bubble. Furthermore, by analyzing the modulations in the ionic current oscillation, the frequency of hydrogen bubble generation that is related to the catalytic efficiency of MoS2 QDs could be estimated. The results reveal the capability of the glass nanopore for the real-time monitoring electrocatalytic behavior, which makes the glass nanopore an ideal candidate to further reveal the heterogeneity of catalytic capability at the single particle level.
- Published
- 2019
21. A Wild-Type Nanopore Sensor for Protein Kinase Activity
- Author
-
Jie Yang, Fu-Na Meng, Yi-Tao Long, and Yi-Lun Ying
- Subjects
Phosphopeptides ,Pore Forming Cytotoxic Proteins ,Bacterial Toxins ,Aerolysin ,010402 general chemistry ,01 natural sciences ,Analytical Chemistry ,Nanopores ,Electricity ,Limit of Detection ,Humans ,Phosphorylation ,Kinase activity ,Protein kinase A ,Protein Kinase Inhibitors ,Kinase ,Drug discovery ,Chemistry ,010401 analytical chemistry ,Wild type ,Cyclic AMP-Dependent Protein Kinases ,0104 chemical sciences ,Nanopore ,Biocatalysis ,MCF-7 Cells ,Biophysics - Abstract
Protein kinases play a critical role in regulating virtually all cellular processes. Here, we developed a novel one-step method based on a wild-type aerolysin nanopore, which enables kinase activity detection without labeling/modification, immobilization, cooperative enzymes and complicated procedures. By virtual of the positively charged confinement of the aerolysin nanopore, the kinase-induced phosphopeptides are specially captured while the positively charged substrate peptides might move away from the pore by the electric field. Combining with internal standard method, the event frequency of the phosphopeptides exhibited a dose-dependent response with kinases. The detection limit of 0.005 U/μL has been achieved with protein kinase A as a model target. This method also allowed kinase inhibitor screening, kinase activity sensing in cell lysates and the real-time monitoring of kinase-catalyzed phosphorylation at singe molecule level, which could further benefit fundamental biochemical research, clinical diagnosis and kinase-targeted drug discovery. Moreover, this nanopore sensor shows strong capacity for the other enzymes that altered substrate charge (e.g., sulfonation, carboxylation, or amidation).
- Published
- 2019
22. Learning Shapelets for Improving Single-Molecule Nanopore Sensing
- Author
-
Hui-Feng Wang, Yi-Lun Ying, Zi-Xuan Wei, Jie Yang, Yi-Tao Long, Jiale Zhou, Meng-Yin Li, and Bing-Yong Yan
- Subjects
Pore Forming Cytotoxic Proteins ,Base Sequence ,Nucleotides ,Chemistry ,Bacterial Toxins ,010401 analytical chemistry ,Nanotechnology ,DNA ,010402 general chemistry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Nanopores ,Nanopore ,Molecule ,Algorithms - Abstract
The nanopore technique employs a nanoscale cavity to electrochemically confine individual molecules, achieving ultrasensitive single-molecule analysis based on evaluating the amplitude and duration of the ionic current. However, each nanopore sensing interface has its own intrinsic sensing ability, which does not always efficiently generate distinctive blockade currents for multiple analytes. Therefore, analytes that differ at only a single site often exhibit similar blockade currents or durations in nanopore experiments, which often produces serious overlap in the resulting statistical graphs. To improve the sensing ability of nanopores, herein we propose a novel shapelet-based machine learning approach to discriminate mixed analytes that exhibit nearly identical blockade current amplitudes and durations. DNA oligomers with a single-nucleotide difference, 5'-AAAA-3' and 5'-GAAA-3', are employed as model analytes that are difficult to identify in aerolysin nanopores at 100 mV. First, a set of the most informative and discriminative segments are learned from the time-series data set of blockade current signals using the learning time-series shapelets (LTS) algorithm. Then, the shapelet-transformed representation of the signals is obtained by calculating the minimum distance between the shapelets and the original signals. A simple logistic classifier is used to identify the two types of DNA oligomers in accordance with the corresponding shapelet-transformed representation. Finally, an evaluation is performed on the validation data set to show that our approach can achieve a high
- Published
- 2019
23. Unveiling the Intrinsic Catalytic Activities of Single‐Gold‐Nanoparticle‐Based Enzyme Mimetics
- Author
-
Wei Ma, Hui Ma, Mahmoud Elsayed Hafez, and Yi-Tao Long
- Subjects
biology ,010405 organic chemistry ,Chemistry ,Nanoparticle ,Ultramicroelectrode ,General Medicine ,General Chemistry ,010402 general chemistry ,Electrocatalyst ,01 natural sciences ,Combinatorial chemistry ,Catalysis ,0104 chemical sciences ,Enzyme catalysis ,Nanomaterials ,Colloidal gold ,biology.protein ,Glucose oxidase - Abstract
Gold nanoparticles (AuNPs) have been demonstrated to serve as effective nanomaterial-based enzyme mimetics (nanozymes) for a number of enzymatic reactions under mild conditions. The intrinsic glucose oxidase and peroxidase activities of single AuNPs and Ag-Au nanohybrids, respectively, were investigated by single NP collision electrochemical measurements. A significantly high turnover number of nanozymes was obtained from individual catalytic events compared with the results from the classical, ensemble-averaged measurements. The unusual enhancement of catalytic activity of single nanozymes is believed to originate from the high accessible surface area of monodispersed NPs and the high activities of carbon-supported NPs during single-particle collision at a carbon ultramicroelectrode. This work introduces a new method for the precise characterization of the intrinsic catalytic activities of nanozymes, giving further insights to the design of high-efficiency nanomaterial catalysts.
- Published
- 2019
24. Detection of structured single‐strand DNA via solid‐state nanopore
- Author
-
Yi-Lun Ying, Shao-Chuang Liu, Yi-Tao Long, and Qiao Li
- Subjects
Electrophoresis ,Materials science ,Clinical Biochemistry ,Solid-state ,DNA, Single-Stranded ,Nanotechnology ,02 engineering and technology ,01 natural sciences ,Biochemistry ,Analytical Chemistry ,Nanopores ,chemistry.chemical_compound ,Molecule ,heterocyclic compounds ,Particle Size ,Analysis method ,010401 analytical chemistry ,Equipment Design ,021001 nanoscience & nanotechnology ,Single Molecule Imaging ,Single strand dna ,0104 chemical sciences ,Quadruplex DNA ,Nanopore ,chemistry ,0210 nano-technology ,DNA - Abstract
Nanopore is a single-molecule analysis method which also employed electrophoresis has achieved promising single-molecule detections. In this study, we designed two kinds of confined spaces by fabricating solid-state nanopores with desirable diameters to study the structured single-strand DNA of C-rich quadruplex. For the nanopore whose diameter is larger than the quadruplex size, the DNA molecule could directly translocate through the nanopore with extremely high speed. For the nanopore whose diameter is smaller than the quadruplex size, DNA molecule which is captured by nanopore could return to the solution without translocation or unzip the quadruplex structure into single-strand and then pass the nanopore. This study certifies that choosing a suitable sensing interface is the vital importance of observing detailed single-molecule information. The solid-state nanopores hold the great potential to study the structural dynamics of quadruplex DNA molecule.
- Published
- 2019
25. Revisiting a classical redox process on a gold electrode by operando ToF-SIMS: where does the gold go?
- Author
-
Xin Hua, Hai-Lun Xia, and Yi-Tao Long
- Subjects
Materials science ,010405 organic chemistry ,General Chemistry ,010402 general chemistry ,Electrochemistry ,01 natural sciences ,Redox ,0104 chemical sciences ,Electrochemical cell ,Chemistry ,chemistry.chemical_compound ,Electron transfer ,chemistry ,Electrode ,Physical chemistry ,Ferricyanide ,Cyclic voltammetry ,Ferrocyanide - Abstract
Our results indicated that a gold electrode participates in the redox reaction of [Fe(CN)6]3/4– by competing with it to form Au(CN)2–., Electrochemical redox conversion between ferricyanide and ferrocyanide on a gold electrode is one of the most classical reactions in electrochemistry. In textbooks, the gold electrode is seen as chemically inert, on which only the adsorption/desorption of [Fe(CN)6]3/4– and electron transfer take place. Here, the electrochemical process of [Fe(CN)6]3/4– on a gold electrode was revisited using a vacuum-compatible microfluidic electrochemical cell in combination with operando liquid ToF-SIMS. An intermediate, Au(CN)2–, was observed in the cyclic voltammetry of ferricyanide with an interesting periodic potential-dependent variation trend. It was demonstrated that the gold electrode participated in the redox reaction of [Fe(CN)6]3/4– by competing with it to form Au(CN)2–, since the formation constant was Fe(CN)63– > Au(CN)2– > Fe(CN)64–. The formation and evolution of Au(CN)2– depends on the ratio of Fe(iii) and Fe(ii) on the surface of the gold electrode, which was determined by the redox conversion between Fe(iii) and Fe(ii) as well as the electric field force-based attraction or repulsion between the gold electrode and [Fe(CN)6]3/4–. Both of these factors were potential-dependent, resulting in the periodic change of Au(CN)2– in the dynamic potential scan of [Fe(CN)6]3/4–. These results provided solid molecular evidence for the participation of the gold electrode in the [Fe(CN)6]3/4– redox system, which will deepen mechanistic understandings of related electrochemical applications.
- Published
- 2019
26. A lithium-ion-active aerolysin nanopore for effectively trapping long single-stranded DNA
- Author
-
Shao-Chuang Liu, Yi-Tao Long, Zheng-Li Hu, Yi-Lun Ying, and Meng-Yin Li
- Subjects
chemistry.chemical_classification ,Oligonucleotide ,Aerolysin ,chemistry.chemical_element ,General Chemistry ,Ion ,Molecular dynamics ,chemistry.chemical_compound ,Nanopore ,chemistry ,Biophysics ,Nucleotide ,Lithium ,DNA - Abstract
Wild-type aerolysin (AeL) nanopores allow direct single nucleotide discrimination of very short oligonucleotides (≤10 nt) without labelling, which shows great potential for DNA sensing. To achieve real applications, one major obstacle of AeL is its poor capture ability of long single-stranded DNA (ssDNA, >10 nt). Here, we have proposed a novel and robust strategy for the electrostatic focusing of long ssDNA into a lithium-chloride (LiCl)-active AeL. By using this method, for the first time we have demonstrated AeL detection of ssDNA longer than 100 nt. Due to screening more negative charges, LiCl improves AeL capture ability of long ssDNA (i.e. 60 nt) by 2.63- to 10.23-fold compared to KCl. Further calculations and molecular dynamics simulations revealed that strong binding between Li+ and the negatively charged residue neutralized the AeL, leading to a reduction in the energy barrier for ssDNA capture. These findings facilitate the future high-throughput applications of AeL in genetic and epigenetic diagnostics.
- Published
- 2019
27. Direct Molecular Evidence of Proton Transfer and Mass Dynamics at the Electrode–Electrolyte Interface
- Author
-
Xin Hua, Yanyan Zhang, Zihua Zhu, Jun-Gang Wang, Fuyi Wang, Xiao-Fei Yu, and Yi-Tao Long
- Subjects
0303 health sciences ,Work (thermodynamics) ,Proton ,Chemistry ,Solvation ,02 engineering and technology ,Electron ,Electrolyte ,021001 nanoscience & nanotechnology ,Electrochemistry ,Ion ,03 medical and health sciences ,Chemical physics ,Electrode ,General Materials Science ,Physical and Theoretical Chemistry ,0210 nano-technology ,030304 developmental biology - Abstract
Proton transfer has been widely regarded as a key step in many electrochemical and biological processes. However, direct molecular evidence has long been lacking. In this work, we chose the electrochemical oxidation of acetaminophen (APAP) as a model system and utilized in situ liquid time-of-flight secondary ion mass spectroscopy (ToF-SIMS) to molecularly examine proton solvation and transfer in this process. In addition, we successfully captured and identified the transient radical intermediate, providing solid molecular evidence to resolve an important debate in electron transfer-proton transfer oxidation mechanism of APAP. Moreover, the potential-dependent behaviors of both inert ions and electroactive species during the dynamic potential scanning were chemically monitored in real time and the mass diffusion mechanism regarding the electroactive and nonelectroactive species was revealed under polarized conditions. The results are consistent with our computer simulations. The observations in this work greatly improved our understanding of proton transfer and mass dynamics occurring at the electrode-electrolyte interface in complex electrochemical processes.
- Published
- 2018
28. Detektieren mit Nanopipetten im eingeschränkten Raum: von einzelnen Molekülen über Nanopartikel hin zu der Zelle
- Author
-
Rui Gao, Ru-Jia Yu, Yi-Lun Ying, and Yi-Tao Long
- Subjects
Chemistry ,02 engineering and technology ,General Medicine ,010402 general chemistry ,021001 nanoscience & nanotechnology ,0210 nano-technology ,01 natural sciences ,0104 chemical sciences - Published
- 2018
29. Direct Sensing of Single Native RNA with a Single-Biomolecule Interface of Aerolysin Nanopore
- Author
-
Ya-Qian Wang, Yi-Tao Long, Jie Yang, Yi-Lun Ying, and Meng-Yin Li
- Subjects
Poly U ,Pore Forming Cytotoxic Proteins ,0301 basic medicine ,Bacterial Toxins ,Lipid Bilayers ,Aerolysin ,Pentose ,Nanopores ,03 medical and health sciences ,chemistry.chemical_compound ,Gene expression ,microRNA ,Electrochemistry ,General Materials Science ,Spectroscopy ,chemistry.chemical_classification ,Chemistry ,Biomolecule ,RNA ,Electrochemical Techniques ,Surfaces and Interfaces ,Condensed Matter Physics ,Aeromonas hydrophila ,Nanopore ,030104 developmental biology ,Phosphatidylcholines ,Biophysics ,Poly A ,DNA - Abstract
RNA sensing is of vital significance to advance our comprehension of gene expression and to further benefit medical diagnostics. Taking advantage of the excellent sensing capability of the aerolysin nanopore as a single-biomolecule interface, we for the first time achieved the direct characterization of single native RNA of Poly(A)4 and Poly(U)4. Poly(A)4 induces ∼10% larger blockade current amplitude than Poly(U)4. The statistical duration of Poly(A)4 is 18.83 ± 1.08 ms, which is 100 times longer than that of Poly(U)4. Our results demonstrated that the capture of RNA homopolymers is restricted by the biased diffusion. The translocation of RNA needs to overcome a lower free-energy barrier than that of DNA. Moreover, the strong RNA-aerolysin interaction is attributed to the hydroxyl in pentose, which prolongs the translocation time. This study opens an avenue for aerolysin nanopores to directly achieve RNA sensing, including discrimination of RNA epigenetic modification and selective detection of miRNA.
- Published
- 2018
30. Highly Sensitive and Selective Electrochemical Detection of Dopamine using Hybrid Bilayer Membranes
- Author
-
Fato Tano Patrice, Da-Wei Li, Li-Jun Zhao, Yi-Tao Long, Essy Kouadio Fodjo, and Kaipei Qiu
- Subjects
Chemistry ,Bilayer ,010401 analytical chemistry ,02 engineering and technology ,Electrochemical detection ,021001 nanoscience & nanotechnology ,Ascorbic acid ,01 natural sciences ,Catalysis ,0104 chemical sciences ,Highly sensitive ,Membrane ,Dopamine ,Electrochemistry ,Biophysics ,medicine ,0210 nano-technology ,Selectivity ,medicine.drug - Published
- 2018
31. Investigation of Lipid Metabolism in Dynamic Progression of Coronary Artery Atherosclerosis of Humans by Time-of-Flight Secondary Ion Mass Spectrometry
- Author
-
Xin Hua, Jiangping Song, Jie Ren, Xiao Chen, Zhan Hu, Min Zhang, Yi-Tao Long, Hao-Wen Li, Hao Cui, and Liang Chen
- Subjects
Linoleic acid ,010401 analytical chemistry ,Spectrometry, Mass, Secondary Ion ,Lipid metabolism ,010402 general chemistry ,Mass spectrometry ,Atherosclerosis ,Lipid Metabolism ,01 natural sciences ,Phenotype ,Coronary Vessels ,Lipids ,0104 chemical sciences ,Analytical Chemistry ,Lesion ,chemistry.chemical_compound ,Metabolic pathway ,chemistry ,Biochemistry ,medicine ,Humans ,Arachidonic acid ,medicine.symptom ,KEGG - Abstract
Alterations in lipid metabolites in coronary artery tissues are phenotypic changes in the progression of atherosclerosis (AS). A full picture of the spatiotemporal distribution of lipid metabolites in coronary AS is needed for a deeper understanding of its pathology and the identification of potential biomarkers of disease progression. In this work, the changes in species, quantity, and distribution of lipid metabolites at different stages of AS, which were standardized by the disease areas, were analyzed through the high spatial resolution- and high sensitivity-time-of-flight secondary ion mass spectrometry (ToF-SIMS) under delayed extraction mode. Based on high lateral resolution imaging, we further analyzed the ToF-SIMS data extracted from the subregions of AS lesion tissues at different disease progression stages by semiquantitative comparison, clustering analysis (t-stochastic neighbor embedding and HCA), and KEGG enrichment. Thus, a much-detailed description of lipids' features in coronary AS was achieved. We constructed a ToF-SIMS mass spectrometry database of coronary AS lipids. 40 specific lipid metabolites with distinctive patterns between different pathological stages were obtained. Chemical imaging unveiled further details regarding the spatial distribution of lipids. Moreover, linoleic acid and arachidonic acid metabolic pathway were predicted to be critical in AS progression.
- Published
- 2021
32. Cover Picture: Diversified exploitation of aerolysin nanopore in single‐molecule sensing and protein sequencing (View 4/2020)
- Author
-
Yi-Lun Ying, Xue-Yuan Wu, Si-Min Lu, Yi-Tao Long, and Meng-Yin Li
- Subjects
Nanopore ,Protein sequencing ,Chemistry ,Aerolysin ,Molecule ,Cover (algebra) ,Computational biology - Published
- 2020
33. Summary and Outlook
- Author
-
Jiajun Wang, Si-Min Lu, Yi-Lun Ying, and Yi-Tao Long
- Subjects
chemistry.chemical_classification ,Nanopore ,chemistry ,Computer science ,Single entity ,Biomolecule ,Measurement science ,High bandwidth ,Nanotechnology - Abstract
Measurement science has been stepping into single entity sensing. Nanopore electrochemistry as a powerful technique is attracting increasing attention for identifying and characterizing single cells, single particles, and even single molecules. Over the past decades, the biological nanopore-based single biomolecule interface has been extensively applied in probing nucleic acids and biomolecular interactions. Thanks to the advanced material science, the development of solid-state nanopores has been greatly promoted, showing new capabilities and features in single molecule analysis and single particle detection. Recently, nanopipettes have exhibited a great advantage in confining strong interactions between pore and analyte, electron-transfer processes and light inside, giving rise to the possibility of adopting nanopore sensing in a wide range of applications, including single-cell manipulating and analysis. Along with the development of nanopore electrochemistry, new data algorithms and high bandwidth instrumentation have also enabled researchers to look deeply into the intrinsic properties of single entities and therefore to associate them with chemical or biological processes. In future, nanopore electrochemistry will open up a new avenue for the better understanding of the chemical and biological world at the single entity level.
- Published
- 2020
34. Single-biomolecule Interface for Advanced Single Molecular Sensors
- Author
-
Jie Yang, Shuang Li, Meng-Yin Li, Ya-Qian Wang, Zheng-Li Hu, Kaipei Qiu, and Yi-Tao Long
- Subjects
chemistry.chemical_classification ,Nanopore ,Analyte ,Materials science ,chemistry ,Clinical diagnosis ,Biomolecule ,Interface (computing) ,Aerolysin ,Nanotechnology ,Protein detection - Abstract
In this chapter, we introduce the biological membrane protein-based single-biomolecule interface for single molecule sensing, including DNA and protein detection, using synergic effects from steric volume exclusion and weak interactions between the nanopore and the analyte. More attentions will be focused on the state-of-art detection strategies for the measurement of a variety of biomolecules via nanopore electrochemistry by the selected experimental case studies, in particular for tracing short-lived metastable conformation and recognition of multiple targets for the promising clinical diagnosis. This chapter selects experimental cases in an α-hemolysin nanopore and an aerolysin nanopore to demonstrate the sensing ability of biological nanopores in detail.
- Published
- 2020
35. Plasmon-Induced Photoreduction System Allows Ultrasensitive Detection of Disease Biomarkers by Silver-Mediated Immunoassay
- Author
-
Xin Hua, Duo Xu, Wei Ma, Yi-Tao Long, Ze-Hui Sun, and Huanxing Han
- Subjects
Fluid Flow and Transfer Processes ,Immunoassay ,Silver ,medicine.diagnostic_test ,Chemistry ,Process Chemistry and Technology ,010401 analytical chemistry ,Metal Nanoparticles ,Bioengineering ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Enzymatic Assays ,Biochemistry ,medicine ,Disease biomarker ,Humans ,0210 nano-technology ,Instrumentation ,Plasmon ,Biomarkers - Abstract
Current strategies for the detection of disease biomarkers often require enzymatic assays that may have limited sensitivity due to inferior stability and vulnerable catalytic activity of the enzyme. A new enzyme-free amplification method for identifying suitable biomarkers is necessary to lower the limit of detection and improve many critical diagnosis applications. Here, we presented an enzyme-free amplified plasmonic immunoassay that enhanced the detection sensitivity of disease biomarkers by combining a novel plasmon-induced silver photoreduction system with a silver nanoparticle (AgNP)-linked immunoassay. The key step to achieving ultrasensitivity was to use Ag
- Published
- 2020
36. Electrochemical Sensing at a Confined Space
- Author
-
Yi-Lun Ying, Si-Min Lu, Yi-Tao Long, and Yue-Yi Peng
- Subjects
Chemistry ,Single entity ,010401 analytical chemistry ,Molecule ,Nanotechnology ,010402 general chemistry ,Electrochemistry ,01 natural sciences ,Confined space ,0104 chemical sciences ,Analytical Chemistry - Abstract
Single entity sensing is recently an area of tremendous inter-est in analytical chemistry, such that it is possible to analyze single cells, single particles, and even single molecules. Among diver...
- Published
- 2020
37. Nanochannels of Covalent Organic Frameworks for Chiral Selective Transmembrane Transport of Amino Acids
- Author
-
Yan Liu, Yong Cui, Rui Gao, Xing Han, Xiaowei Wu, Yi-Tao Long, and Chen Yuan
- Subjects
chemistry.chemical_classification ,Aldehydes ,Molecular Structure ,Chemistry ,Surface Properties ,Biological Transport ,General Chemistry ,Membrane transport ,Diamines ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Combinatorial chemistry ,Catalysis ,0104 chemical sciences ,Amino acid ,Colloid and Surface Chemistry ,Covalent bond ,Nanotechnology ,Imines ,Amino Acids ,Particle Size ,human activities ,Porosity ,ComputingMethodologies_COMPUTERGRAPHICS - Abstract
Mimicking cellular transport mechanisms to make solid-state smart nanochannels has long been of great interest for their diverse applications, but it poses a critical synthetic challenge. Covalent organic frameworks (COFs) are porous crystalline materials with tailor-made nanochannels and hold great potential for ion and molecule transport. We demonstrate here for the first time that 2D COFs possess the necessary merits to be promising solid-state nanochannels for selective transport of amino acids, which are the basis for life. By imine condensations of a
- Published
- 2019
38. Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface
- Author
-
Ya-Qian Wang, Jiajun Wang, Yi-Lun Ying, Xue-Yuan Wu, Jin Huang, Yi-Tao Long, Meng-Yin Li, and Jie Yang
- Subjects
chemistry.chemical_classification ,Oligonucleotide ,Mutant ,Aerolysin ,DNA sequencing ,Lesion ,Nanopore ,chemistry.chemical_compound ,chemistry ,Biophysics ,medicine ,Nucleotide ,medicine.symptom ,DNA - Abstract
DNA lesion such as metholcytosine(mC), 8-OXO-guanine(OG), inosine(I) etc could cause the genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (mC, OG, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.
- Published
- 2019
39. A Nanopore Phosphorylation Sensor for Single Oligonucleotides and Peptides
- Author
-
Yi-Lun Ying, Jie Yang, Fu-Na Meng, Yi-Tao Long, Shuang Li, and Meng-Ying Li
- Subjects
chemistry.chemical_classification ,Multidisciplinary ,010405 organic chemistry ,Oligonucleotide ,Kinase ,Chemistry ,Science ,Phosphatase ,Aerolysin ,Peptide ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Dephosphorylation ,Nanopore ,Biophysics ,Phosphorylation ,0210 nano-technology ,Research Article - Abstract
The phosphorylation of oligonucleotides and peptides plays a critical role in regulating virtually all cellular processes. To fully understand these complex and fundamental regulatory pathways, the cellular phosphorylate changes of both oligonucleotides and peptides should be simultaneously identified and characterized. Here, we demonstrated a single-molecule, high-throughput, label-free, general, and one-step aerolysin nanopore method to comprehensively evaluate the phosphorylation of both oligonucleotide and peptide substrates. By virtue of electrochemically confined effects in aerolysin, our results show that the phosphorylation accelerates the traversing speed of a negatively charged substrate for about hundreds of time while significantly enhances the translocation frequency of a positively charged substrate. Thereby, the kinase/phosphatase activity could be directly measured with the aerolysin nanopore from the characteristically dose-dependent event frequency of the substrates. By using this straightforward approach, a model T 4 oligonucleotide kinase (PNK) further achieved the nanopore evaluation of its phosphatase activity and real-time monitoring of its phosphatase-catalyzed dephosphorylation at a single-molecule level. Our study provides a step forward to nanopore enzymology for analyzing the phosphorylation of both oligonucleotides and peptides with significant feasibility in fundamental biochemical researches, clinical diagnosis, and kinase/phosphatase-targeted drug discovery.
- Published
- 2019
40. Controllable Aggregation-Induced Exocytosis Inhibition (CAIEI) of Plasmonic Nanoparticles in Cancer Cells Regulated by MicroRNA
- Author
-
Yi-Tao Long, Jian Lv, and Ruo-Can Qian
- Subjects
Metal Nanoparticles ,Pharmaceutical Science ,Nanoparticle ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Exocytosis ,Exocytosis Inhibition ,Drug Discovery ,microRNA ,Humans ,Nanotechnology ,Plasmonic nanoparticles ,Chemistry ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,MicroRNAs ,Colloidal gold ,Cancer cell ,MCF-7 Cells ,Biophysics ,Molecular Medicine ,Gold ,0210 nano-technology ,Intracellular - Abstract
Recent advances in nanotechnology have produced plenty of intracellular drug delivery systems based on various functional nanoparticles. Although much progress has been achieved in improving cellular uptake efficiency, the retention time of these engineered nanoparticles in living cells has not yet received wide attention. Here, we report the controllable exocytosis of plasmonic gold nanoparticles (GNPs) based on a microRNA-21 (miRNA-21) targeted binary system. Rapid intracellular accumulation of GNPs was observed in miRNA-21 positive MCF-7 breast cancer cells, which blocked the exocytosis of the GNP aggregates. Under near-infrared (NIR) irradiation, MCF-7 cells were successfully killed due to the far-red and NIR absorption of the GNP aggregates. In contrast, in miRNA-21 negative cells, the dispersive GNPs escaped from the cells after 6 h. The traces of GNPs could be conveniently captured under the dark-field microscope. This work provides a promising platform for the study of controllable aggregation-induced exocytosis inhibition (CAIEI) of nanocarriers, which is inspiring for the design of more effective nanodrugs for the treatment of cancer.
- Published
- 2018
41. Investigation of the Ionization Mechanism of NAD+/NADH-Modified Gold Electrodes in ToF-SIMS Analysis
- Author
-
Yi-Tao Long, Li-Jun Zhao, and Xin Hua
- Subjects
Nicotinamide ,Sodium ,chemistry.chemical_element ,02 engineering and technology ,Nicotinamide adenine dinucleotide ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Photochemistry ,01 natural sciences ,Pyrophosphate ,0104 chemical sciences ,Secondary ion mass spectrometry ,chemistry.chemical_compound ,chemistry ,Structural Biology ,Ionization ,Mass spectrum ,NAD+ kinase ,0210 nano-technology ,Spectroscopy - Abstract
Analysis of nicotinamide adenine dinucleotide (NAD+/NADH)-modified electrodes is important for in vitro monitoring of key biological processes. In this work, time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to analyze NAD+/NADH-modified gold electrodes. Interestingly, no obvious characteristic peaks of nicotinamide fragment could be observed in the mass spectra of NAD+/NADH in their neutral sodium pyrophosphate form. However, after acidification, the characteristic peaks for both NAD+ and NADH were detected. This was due to the suppression effect of inner pyrophosphoric salts in both neutral molecules. Besides, it was proved that the suppression by inner salt was intramolecular. No obvious suppression was found between neighboring molecules. These results demonstrated the suppression effect of inner salts in ToF-SIMS analysis, providing useful evidence for the study of ToF-SIMS ionization mechanism of organic molecule-modified electrodes. Graphical Abstract ᅟ.
- Published
- 2018
42. Real-time Event Recognition and Analysis System for Nanopore Study
- Author
-
Hui-Feng Wang, Fei Huang, Zheng-Li Hu, Yi-Lun Ying, Zhen Gu, Yi-Tao Long, and Bing-Yong Yan
- Subjects
Data processing ,Finite impulse response ,Chemistry ,Event recognition ,010401 analytical chemistry ,Bandwidth (signal processing) ,Ranging ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Nanopore ,Electronic engineering ,Software system ,Weak current ,0210 nano-technology - Abstract
To achieve fast and accurate analysis of weak current signal of nanopore-based single molecule detection, an online data process based on adaptive threshold algorithm with data buffering technique and finite impulse response filtering was designed. A software system based on the data process was developed for online recognition and analysis of nanopore events during nanopore experiment. To testify the performance of the algorithm and software system, ideal signals with different noise level (20–100 pA) were generated at bandwidth ranging from 3 kHz to 100 kHz. The result showed that this software system was stable at different bandwidths and sampling rates and could be used in analyzing the signals at high noise. The proposed software system was further applied to aerolysin nanopore experiment for detection of poly(dA)4 molecules. The results showed that the data process system could be applied in real nanopore recording experiment with high accuracy and speed.
- Published
- 2018
43. Detection of Peptides with Different Charges and Lengths by Using the Aerolysin Nanopore
- Author
-
Shuang Li, Chan Cao, Yi-Tao Long, and Jie Yang
- Subjects
0301 basic medicine ,chemistry.chemical_classification ,Chemistry ,Aerolysin ,Peptide ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Catalysis ,03 medical and health sciences ,Nanopore ,030104 developmental biology ,Electrochemistry ,Biophysics ,0210 nano-technology - Published
- 2018
44. Individual Modified Carbon Nanotube Collision for Electrocatalytic Oxidation of Hydrazine in Aqueous Solution
- Author
-
Fato Tano Patrice, Yi-Tao Long, Li-Jun Zhao, Kaipei Qiu, Da-Wei Li, and Essy Kouadio Fodjo
- Subjects
Nanotube ,Aqueous solution ,Inorganic chemistry ,Ultramicroelectrode ,02 engineering and technology ,Buffer solution ,Chronoamperometry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,chemistry.chemical_compound ,Pyrroloquinoline quinone ,chemistry ,Catalytic oxidation ,General Materials Science ,Cyclic voltammetry ,0210 nano-technology - Abstract
Collision at a single molecule level was achieved based on the nanoimpact of an individual pyrroloquinoline quinone (PQQ) modified multiwalled carbon nanotube (MWCNT) at the carbon fiber ultramicroelectrode (C UME). Electrocatalytic amplification of the current responses was observed when the PQQ-modified MWCNT collided with C UME in the presence of hydrazine (N2H4) in a Tris-HCl buffer solution, which was also supported by the conventional cyclic voltammetry and chronoamperometry techniques. The enhanced catalytic oxidation of N2H4 was due to the “addition-elimination” redox cycling mechanism of PQQ/PQQH2, where the oxidation of N2H4 occurred together with the reduction of PQQ under an external bias, and the formed PQQH2 intermediate would be reoxidized back to PQQ simultaneously. The average collision current, duration, and charge for PQQ-modified MWCNT at 1.0 V vs Ag/AgCl were 105 pA, 0.45 ms, and 49 fC, respectively. As a result, the turnover frequency of electrocatalytic oxidation of N2H4 by PQQ was ...
- Published
- 2018
45. Monitoring disulfide bonds making and breaking in biological nanopore at single molecule level
- Author
-
Chan Cao, Yi-Tao Long, Da-Wei Li, Ya-Qian Wang, and Bing Zhou
- Subjects
DTNB ,Chemistry ,Aerolysin ,Ionic bonding ,02 engineering and technology ,General Chemistry ,Nanoreactor ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Reversible reaction ,0104 chemical sciences ,Nanopore ,Chemical bond ,Biophysics ,Molecule ,0210 nano-technology - Abstract
Monitoring subtle changes in ionic current flow through a nanopore could be applied to observe single molecule reaction. Here, we introduced cysteine to substitute for lysine at position 238 constructing a mutant aerolysin K238C. It could be regarded as a nanoreactor to efficiently visualize chemical bonds making and breaking. The compound 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB) was selected as a reactant coming into collisions on the interface of the pore to occur a reversible reaction. Our results showed that the mutant aerolysin could respond to three molecules of DTNB simultaneously and reflect corresponding levels with distinguishable current signals. Therefore, this method constitutes a simple, generic tool for monitoring single molecule reaction, which evokes a guidance for the mutant aerolysin towards the application of tracking other more reactions at single molecule level.
- Published
- 2018
46. Quantifying Visible-Light-Induced Electron Transfer Properties of Single Dye-Sensitized ZnO Entity for Water Splitting
- Author
-
Wei Ma, Yi-Tao Long, Yue-Yi Peng, Hui Ma, Zhe-Yao Yang, He Tian, Jianfu Chen, and Xiao-Yuan Liu
- Subjects
Photocurrent ,Chemistry ,business.industry ,Ultramicroelectrode ,02 engineering and technology ,General Chemistry ,Electron ,010402 general chemistry ,021001 nanoscience & nanotechnology ,01 natural sciences ,Biochemistry ,Electron transport chain ,Catalysis ,Photoinduced electron transfer ,0104 chemical sciences ,Electron transfer ,Colloid and Surface Chemistry ,Optoelectronics ,Water splitting ,0210 nano-technology ,business ,Photocatalytic water splitting - Abstract
Quantifying the photoinduced electron transfer properties of a single entity is of paramount importance for clarifying the link between the photoelectrochemical performance and the specific properties of an individual. Here, we successfully monitored the photoelectrochemical behavior of a single dye-sensitized ZnO entity on a Au ultramicroelectrode with different TiO2 film thicknesses. Due to a trap-limited electron diffusion in TiO2 film, a sub-millisecond photocurrent transient was observed for an individual N719@ZnO associated with single-particle photocatalytic water splitting. Furthermore, a Monte Carlo random walk numerical simulation model was developed to simulate the photoinjected electron transport dynamics and recombination in a nanoparticulate TiO2 film. Our approach allowed the photocatalytic properties of N719 at the single-molecule level to be quantified, and electron diffusivity and electron collection efficiency as a function of the film thickness were estimated by simulation analyses. Ex...
- Published
- 2018
47. Electrochemically generated green-fluorescent N-doped carbon quantum dots for facile monitoring alkaline phosphatase activity based on the Fe3+-mediating ON-OFF-ON-OFF fluorescence principle
- Author
-
Yi-Tao Long, Yuanhong Xu, Fushuang Niu, Xin Hua, Yi-Lun Ying, and Yusheng Niu
- Subjects
Detection limit ,Quantum yield ,Ethylenediamine ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Electrochemistry ,01 natural sciences ,Fluorescence ,Pyrophosphate ,0104 chemical sciences ,chemistry.chemical_compound ,Hydrolysis ,chemistry ,Biochemistry ,Alkaline phosphatase ,General Materials Science ,0210 nano-technology ,Nuclear chemistry - Abstract
Herein, green-fluorescent N-doped carbon quantum dots (N-CQDs) with quantum yield of 30.6% were prepared via a simple bottom-up electrochemical (EC) method using the mixtures of pyrocatechol and ethylenediamine as both precursors and electrolytes. The ON-OFF fluorescence (FL) principle that the FL intensity of the N-CQDs was quenched in the presence of Fe3+ was further extended to the ON-OFF-ON and ON-OFF-ON-OFF ones for pyrophosphate anions (PPi) and alkaline phosphatase (ALP) detection, respectively, based on the specific competitive interaction of N-CQDs with Fe3+ and PPi and the hydrolysis of PPi in the presence ALP. Under the optimized conditions, limit of detection (LOD) of 1.2 μM and 0.5 μM were achieved for assays of Fe3+ and PPi, respectively. Meanwhile, measurable evaluation of ALP activity was reached in a wide range from 5 to 360 U/L with a LOD of 1.1 U/L. The as-proposed sensors showed many advantages including label free, rapid, simple, low-cost, high sensitive, which has great promising application potential in vivo and in vitro clinical diagnosis and will promote the application of EC derived carbon nanomaterials.
- Published
- 2018
48. Glypican-3-targeted precision diagnosis of hepatocellular carcinoma on clinical sections with a supramolecular 2D imaging probe
- Author
-
Wen Wen, He Tian, Yu-Jiao Qiu, Yuan-Yuan Shi, Hai-Hao Han, Li-Wei Dong, Hongyang Wang, Yexiong Tan, Yi-Tao Long, and Xiao-Peng He
- Subjects
Carcinoma, Hepatocellular ,Time Factors ,Pathology, Surgical ,Medicine (miscellaneous) ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,Glypican 3 ,Glypicans ,Biomarkers, Tumor ,medicine ,Humans ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,Frozen section procedure ,biology ,Diagnostic Tests, Routine ,Chemistry ,Liver Neoplasms ,021001 nanoscience & nanotechnology ,medicine.disease ,Fluorescence ,Molecular Imaging ,0104 chemical sciences ,Staining ,Biomarker (cell) ,Hepatocellular carcinoma ,Cancer cell ,Cancer research ,biology.protein ,Antibody ,0210 nano-technology - Abstract
The ability of chemical tools to effectively detect malignancy in frozen sections removed from patients during surgery is important for the timely determination of the subsequent surgical program. However, current clinical methods for tissue imaging rely on dye-based staining or antibody-based techniques, which are sluggish and complicated. Methods: Here, we have developed a 2D material-based supramolecular imaging probe for the simple, rapid yet precise diagnosis of hepatocellular carcinoma (HCC). The 2D probe is constructed through supramolecular self-assembly between a water soluble, fluorescent peptide ligand that selectively targets glypican-3 (GPC-3, a specific cell-surface biomarker for HCC) and 2D molybdenum disulfide that acts as a fluorescence quencher as well as imaging enhancer. Results: We show that the 2D imaging probe developed with minimal background fluorescence can sensitively and selectively image cells overexpressing GPC-3 over a range of control cells expressing other membrane proteins. Importantly, we demonstrate that the 2D probe is capable of rapidly (signal became readable within 1 min) imaging HCC tissues over para-carcinoma regions in frozen sections derived from HCC patients; the results are in accordance with those obtained using traditional clinical staining methods. Conclusion: Compared to conventional staining methods, which are laborious (e.g., over 30 min is needed for antibody-based immunosorbent assays) and complex (e.g., diagnosis is based on discrimination of the nucleus morphology of cancer cells from that of normal cells), our probe, with its simplicity and quickness, might become a promising candidate for tumor-section staining as well as fluorescence imaging-guided surgery.
- Published
- 2018
49. Reversible redox inter-conversion of biologically active NAD+/NADH derivatives bound to a gold electrode: ToF-SIMS evidence
- Author
-
Ruo-Can Qian, Xin Hua, Yi-Tao Long, Jian Lv, and Li-Jun Zhao
- Subjects
Nad nadh ,Chemistry ,Metals and Alloys ,Biological activity ,02 engineering and technology ,General Chemistry ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Electrochemistry ,01 natural sciences ,Combinatorial chemistry ,Redox ,Catalysis ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Secondary ion mass spectrometry ,Electrode ,Materials Chemistry ,Ceramics and Composites ,Surface modification ,NAD+ kinase ,0210 nano-technology - Abstract
The realization of the reversible inter-conversion between NADH and NAD+ is a long-term challenge in biological and energy-related chemistry. Here, we achieve the electrochemical reversible redox of NAD+/NADH derivatives by the functionalization of a gold electrode with a specially designed NAD+ derivative, and the electrochemical redox products are characterized by time-of-flight secondary ion mass spectrometry (ToF-SIMS).
- Published
- 2018
50. Metal/Matrix Enhanced Time-of-flight Secondary Ion Mass Spectrometry for Single Cell Lipids Analysis
- Author
-
Hao-Wen Li, Yi-Tao Long, and Xin Hua
- Subjects
Delayed extraction ,chemistry.chemical_classification ,Resolution (mass spectrometry) ,Chemistry ,Biomolecule ,010401 analytical chemistry ,Substrate (chemistry) ,02 engineering and technology ,021001 nanoscience & nanotechnology ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Secondary ion mass spectrometry ,Matrix (chemical analysis) ,Single-cell analysis ,Mass spectrum ,Biophysics ,0210 nano-technology - Abstract
The chemical components analysis of single cell is important for the understanding of physiological processes such as cell growth, signal transduction and apoptosis. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a sensitive surface analysis technique with high spatial resolution, which has been used for single cell and micro-area analysis. However, relatively low ionization yield of biomolecules limited its wide applications in single cell analysis. Herein, we used metal substrate and matrix material to enhance the ionization yield of lipids. The signal intensity of phosphatidylcholine (PC 40:0) casted on the matrix/gold-coated silicon substrate was 65 times higher than that on the silicon wafer. The signal enhancement of phosphatidylcholine (PC 34:1) on single cell surface cultured on matrix/gold-coated silicon substrate was observed as well. Owing to the influence of irregular topography and complex chemical environment of cell, the increase of lipids signal was smaller. Delayed extraction mode of ToF-SIMS overcame the effects of cell topography, leading to further enhancement of the signal intensity of lipids. Meanwhile, simultaneous high spatial resolution of chemical imaging and high mass resolution of the mass spectra of single cells were obtained. Our strategies provided new insights into the study of cell metabolism and cell-environment interactions.
- Published
- 2018
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.