Electrochemical analysis of single molecules is a method with the strong ability of the enhanced efficiency and ultra-sensitivity.Here,we demonstrate that the electrochemical confined space could efficiently convert s...Electrochemical analysis of single molecules is a method with the strong ability of the enhanced efficiency and ultra-sensitivity.Here,we demonstrate that the electrochemical confined space could efficiently convert single molecule characteristics into measurable electrochemical signatures with high temporal resolution.The human telomere repeat sequence T8 was used as a probe to determine the electrochemical confined effect in a nanopore.Our results show that the nanopore with comparable confined space of the telomere repeat sequence exhibits the most distinguishable single-molecule signals which suggest the folded conformation of T8.This method will greatly extend the lifetime of a metastable conformation for a single biomolecule by strong analyte-nanopore interactions,which brings the new insight into the understanding of the biomolecule's function at single-molecule level.展开更多
Nanopore-based techniques have attracted increasing attention as a unique tool for single-molecule analysis.To accurately detect individual motions of each single molecule,nanopore techniques are used to develop an ul...Nanopore-based techniques have attracted increasing attention as a unique tool for single-molecule analysis.To accurately detect individual motions of each single molecule,nanopore techniques are used to develop an ultrasensitive current measurement system.This work proposes an integrated current measurement system containing an amplifier system and a current signal acquisition system with a high current resolution and a high temporal resolution for nanopore analysis.The exploration and achievements in instrument and signal processing endow nanopore techniques with reliability,affordability,and portability,which make a great leap toward its real applications.展开更多
Nanopores employ the ionic current from the single molecule blockage to identify the structure,conformation,chemical groups and charges of a single molecule.Despite the tremendous development in designing sensitive po...Nanopores employ the ionic current from the single molecule blockage to identify the structure,conformation,chemical groups and charges of a single molecule.Despite the tremendous development in designing sensitive pore-forming materials,at some extent,the analyte with the single group difference still exhibits similar residual current or duration time.The serious overlap in the statistical results of residual current and duration time brings the difficulties in the nanopore discrimination of each single molecules from the mixture.In this paper,we present the AdaBoost-based machine learning model to identify the multiple analyte with single group difference in the mixed blockages.A set of feature vectors which is obtained from Hidden Markov Model(HMM)is used to train the AdaBoost model.By employing the aerolysin sensing of 5ʹ-AAAA-3ʹ(AA3)and 5ʹ-GAAA-3ʹ(GA3)as the model system,our results show that AdaBoost model increases the identification accu-racy from~0.293 to above 0.991.Furthermore,five sets of mixed blockages of AA3 and GA3 further validate the average accuracy of training and validation,which are 0.997 and 0.989,respectively.The proposed methods improve the capacity of wild-type biological nanopore in efficiently identify the single nucleotide difference without designing of protein and optimizing of the experimental condition.Therefore,the AdaBoost-based machine learning approach could promote the nanopore practical application such as genetic and epigenetic detection.展开更多
We presented an integrated software system for analyzing nanopore data.This self-developed software provided rapid processes for accurate location,classification,and evaluation of every individual blockade.Using the p...We presented an integrated software system for analyzing nanopore data.This self-developed software provided rapid processes for accurate location,classification,and evaluation of every individual blockade.Using the proposed software,statistical analysis could be achieved easily and conveniently.The results of β-Amyloid 42 demonstrated that our data process could rapidly extract duration time and current amplitudes.In addition,our data process could accurately carry out statistical fittings.展开更多
Nanopore technique enables a sensitive, label free, low cost and high throughput method for single-molecule analysis[1–4]. Usually, the nanopore is fabricated on an insulating membrane with electrolyte solution in tw...Nanopore technique enables a sensitive, label free, low cost and high throughput method for single-molecule analysis[1–4]. Usually, the nanopore is fabricated on an insulating membrane with electrolyte solution in two sides, which can act as the only pathway for the ionic flow. When a single molecule enters the pore under the applied biased potential, it will temporarily block the ionic current flow through the nanopore. By analyzing the amplitude, duration, shape and frequency spectra of ionic current modulations, nanopore detection could provide the characteristics of the analytes.展开更多
Nanopore technique plays an important role in single molecule detection, which illuminates the properties of an individual molecule by analyzing the blockage durations and currents. However, the traditional exponentia...Nanopore technique plays an important role in single molecule detection, which illuminates the properties of an individual molecule by analyzing the blockage durations and currents. However, the traditional exponential function is lack of efficiency to describe the distributions of blockage durations in nanopore experiments. Herein, we introduced an exponentially modified Gaussian （EMG） function to fit the duration histograms of both simulated events and experimental events. In comparison with the traditional exponential function, our results demonstrated that the EMG provides a better fit while covers the entire range of the distributions. In particular, the fitted parameters of EMG could be directly used to discriminate the sequence length of the oligonucleotides at single molecule level.展开更多
The size distribution and molecular structure of water clusters play a critical role in the chemical,biological and atmospheric process.The common experimental study of water clusters in aqueous solution is challenged...The size distribution and molecular structure of water clusters play a critical role in the chemical,biological and atmospheric process.The common experimental study of water clusters in aqueous solution is challenged due to the influence of local H-bonding environments on vibration spectroscopies or vacuum requirements for most mass spectrometry technologies.Here,the time-of-flight secondary ion mass spectrometry（To F-SIMS）combining with a microfluidic chip has been applied to achieve the in-situ discrimination of the size distribution for water clusters in liquid water at room temperature.The results demonstrated that the presented method is highly system stable,reproducible and accurate.The comparison of heavy water with pure water was made to further demonstrate the accuracy of this technique.These results showed that（H2O）3H-＋ and （D2O）4D-＋ are the most dominant clusters in pure and heavy water,respectively.This one water molecule difference in the dominant cluster size may due to the nuclear quantum effects on water’s hydrogen bonded network.It is the first time to experimentally show the size distribution of water clusters over a wide range（n=1–30）for pure展开更多
Membrane protein molecules can self-assemble to form a single-biomolecule interface,which can accommodate one single molecule at a time and provide a suitable sensing environment for single-molecule measurements.To ac...Membrane protein molecules can self-assemble to form a single-biomolecule interface,which can accommodate one single molecule at a time and provide a suitable sensing environment for single-molecule measurements.To achieve the high temporal and spatial resolution for revealing the heterogenous of single molecules,one of the most important challenge is to construct a functional single-biomolecule interface.展开更多
Nanopore is an ultra-sensitive electrochemical technique for single molecular detection in confined space. To suppress the noise in detection of the weak current of nanopore, we investigated the influence of membrane ...Nanopore is an ultra-sensitive electrochemical technique for single molecular detection in confined space. To suppress the noise in detection of the weak current of nanopore, we investigated the influence of membrane capacitance and applied voltage on the noise of the current signal by model analysis, simulation and experiment. The obtained results demonstrated that membrane capacitance affects the noise by amplifying the noise of the applied voltage. Therefore, suppression of applied voltage noise is an efficient approach for reducing the noise in nanopore detection. Here, we developed an ultra-low noise instrument system for detecting the single molecule signal in nanopores. As demonstrated by nanopore experiments, the p-p noise of the developed system during the recording is reduced to 3.2B pA using the filter of 5 kHz. Therefore, the developed system could be applied in highly sensitive nanopore detection.展开更多
Measurements at the single-entity level provide more precise diagnosis and understanding of basic biological and chemical processes.Recent advances in the chemical measurement provide a means for ultra-sensitive analy...Measurements at the single-entity level provide more precise diagnosis and understanding of basic biological and chemical processes.Recent advances in the chemical measurement provide a means for ultra-sensitive analysis.Confining the single analyte and electrons near the sensing interface can greatly enhance the sensitivity and selectivity.In this review,we summarize the recent progress in single-entity electrochemistry of single molecules,single particles,single cells and even brain analysis.The benefits of confining these entities to a compatible size sensing interface are exemplified.Finally,the opportunities and challenges of single entity electrochemistry are addressed.展开更多
Main observation and conclusion Single nanoparticle collision has attracted great attention in the last several years to reveal the electron transfer and motion trajectories of individual particles at the electrode su...Main observation and conclusion Single nanoparticle collision has attracted great attention in the last several years to reveal the electron transfer and motion trajectories of individual particles at the electrode surface.An envelope algorithm is proposed for further reading and demonstrating the corresponding current signals.展开更多
Nanopore techniques are experiencing a gallop since it walked out the notebook and show its charm on the science arena.The nanoscale pore offers a single-molecule resolution with a label-free and high-selective manner...Nanopore techniques are experiencing a gallop since it walked out the notebook and show its charm on the science arena.The nanoscale pore offers a single-molecule resolution with a label-free and high-selective manner for the research of molecular structures,molecular dynamics,single-molecule reactions and for a variety of applications in biophysics and bionanotechnology.In this review,we introduce the construction of three types of nanopore platforms along with the latest progress in DNA sensing,structure and dynamics analysis of peptides/proteins,and the detection of redox reactions with new sensing mechanisms.Then,we depict nanopore data processing methods which provide an insight of data mining under the background ofbig data.We could fully expect the great impact of nanopore techniques on not only for DNA sequencing and sensing applications,but also in protein sequencing and clinical diagnostics.展开更多
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 phosphorylat...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,highthroughput,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 T4 oligonucleotide kinase(PNK)further achieved the nanopore evaluation of its phosphatase activity and real-time monitoring of its phosphatase-catalyzed dephosphorylation at a singlemolecule 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.展开更多
Ratiometric probes facilitate quantitative studies via self-calibration and are cherished for bioimaging.Often,a small probe-product spectral separation leads to crosstalk,but the rational development of ratiometric p...Ratiometric probes facilitate quantitative studies via self-calibration and are cherished for bioimaging.Often,a small probe-product spectral separation leads to crosstalk,but the rational development of ratiometric probes with zero probe-product crosstalk remains challenging.Harnessing the recent progress on photophysical modulation of xanthenoid fluorochromes,we propose a powerful and versatile probe design principle,that is,“bridging-group modification,”and developed totalROX,a robust probe for monitoring the total cellular oxidative capacity.展开更多
基金supported by the National Natural Science Foundation of China(21421004,21505043,21327807)the Fundamental Research Funds for the Central Universities(222201718001,222201717003,222201714012)
文摘Electrochemical analysis of single molecules is a method with the strong ability of the enhanced efficiency and ultra-sensitivity.Here,we demonstrate that the electrochemical confined space could efficiently convert single molecule characteristics into measurable electrochemical signatures with high temporal resolution.The human telomere repeat sequence T8 was used as a probe to determine the electrochemical confined effect in a nanopore.Our results show that the nanopore with comparable confined space of the telomere repeat sequence exhibits the most distinguishable single-molecule signals which suggest the folded conformation of T8.This method will greatly extend the lifetime of a metastable conformation for a single biomolecule by strong analyte-nanopore interactions,which brings the new insight into the understanding of the biomolecule's function at single-molecule level.
基金supported by the National Natural Science Foundation of China(21327807)funds from the National Science Fund for Distinguished Young Scholars of China(21125522)
文摘Nanopore-based techniques have attracted increasing attention as a unique tool for single-molecule analysis.To accurately detect individual motions of each single molecule,nanopore techniques are used to develop an ultrasensitive current measurement system.This work proposes an integrated current measurement system containing an amplifier system and a current signal acquisition system with a high current resolution and a high temporal resolution for nanopore analysis.The exploration and achievements in instrument and signal processing endow nanopore techniques with reliability,affordability,and portability,which make a great leap toward its real applications.
基金This research was supported by the National Natural Science Foundation of China(6187118,2183400 and 21711530216)the“Chen Guang”project supported by Shanghai Municipal Education Commission and Shanghai Education Development Foundation(17CG27).
文摘Nanopores employ the ionic current from the single molecule blockage to identify the structure,conformation,chemical groups and charges of a single molecule.Despite the tremendous development in designing sensitive pore-forming materials,at some extent,the analyte with the single group difference still exhibits similar residual current or duration time.The serious overlap in the statistical results of residual current and duration time brings the difficulties in the nanopore discrimination of each single molecules from the mixture.In this paper,we present the AdaBoost-based machine learning model to identify the multiple analyte with single group difference in the mixed blockages.A set of feature vectors which is obtained from Hidden Markov Model(HMM)is used to train the AdaBoost model.By employing the aerolysin sensing of 5ʹ-AAAA-3ʹ(AA3)and 5ʹ-GAAA-3ʹ(GA3)as the model system,our results show that AdaBoost model increases the identification accu-racy from~0.293 to above 0.991.Furthermore,five sets of mixed blockages of AA3 and GA3 further validate the average accuracy of training and validation,which are 0.997 and 0.989,respectively.The proposed methods improve the capacity of wild-type biological nanopore in efficiently identify the single nucleotide difference without designing of protein and optimizing of the experimental condition.Therefore,the AdaBoost-based machine learning approach could promote the nanopore practical application such as genetic and epigenetic detection.
基金supported by the National Natural Science Foundation of China(21327807)Y.-T.Long is grateful for funds from the National Science Fund for Distinguished Young Scholars of China(21125522)
文摘We presented an integrated software system for analyzing nanopore data.This self-developed software provided rapid processes for accurate location,classification,and evaluation of every individual blockade.Using the proposed software,statistical analysis could be achieved easily and conveniently.The results of β-Amyloid 42 demonstrated that our data process could rapidly extract duration time and current amplitudes.In addition,our data process could accurately carry out statistical fittings.
基金supported by the National Natural Science Foundation of China (21327807, 21421004)the “Chen Guang” project from Shanghai Municipal Education Commission and Shanghai Education Development Foundation (7CG27)+1 种基金Innovation Program of Shanghai Municipal Education Commission (2017-01-07-00-02-E00023)the Fundamental Research Funds for the Central Universities (222201718001, 222201717003)
文摘Nanopore technique enables a sensitive, label free, low cost and high throughput method for single-molecule analysis[1–4]. Usually, the nanopore is fabricated on an insulating membrane with electrolyte solution in two sides, which can act as the only pathway for the ionic flow. When a single molecule enters the pore under the applied biased potential, it will temporarily block the ionic current flow through the nanopore. By analyzing the amplitude, duration, shape and frequency spectra of ionic current modulations, nanopore detection could provide the characteristics of the analytes.
基金the National Natural Science Foundation of China(No.21327807)the National Science Fund for Distinguished Young Scholars of China(No.21125522)
文摘Nanopore technique plays an important role in single molecule detection, which illuminates the properties of an individual molecule by analyzing the blockage durations and currents. However, the traditional exponential function is lack of efficiency to describe the distributions of blockage durations in nanopore experiments. Herein, we introduced an exponentially modified Gaussian （EMG） function to fit the duration histograms of both simulated events and experimental events. In comparison with the traditional exponential function, our results demonstrated that the EMG provides a better fit while covers the entire range of the distributions. In particular, the fitted parameters of EMG could be directly used to discriminate the sequence length of the oligonucleotides at single molecule level.
基金supported by the National Natural Science Foundation of China (21421004, 21705046)Innovation Program of Shanghai Municipal Education Commission (2017-01-07-00-02E00023)+2 种基金the Programme of Introducing Talents of Discipline to Universities (B16017)the Program of Shanghai Subject Chief Scientist (15XD1501200)the Fundamental Research Funds for the Central Universities (222201718001, 222201717003, 222201714012)
文摘The size distribution and molecular structure of water clusters play a critical role in the chemical,biological and atmospheric process.The common experimental study of water clusters in aqueous solution is challenged due to the influence of local H-bonding environments on vibration spectroscopies or vacuum requirements for most mass spectrometry technologies.Here,the time-of-flight secondary ion mass spectrometry（To F-SIMS）combining with a microfluidic chip has been applied to achieve the in-situ discrimination of the size distribution for water clusters in liquid water at room temperature.The results demonstrated that the presented method is highly system stable,reproducible and accurate.The comparison of heavy water with pure water was made to further demonstrate the accuracy of this technique.These results showed that（H2O）3H-＋ and （D2O）4D-＋ are the most dominant clusters in pure and heavy water,respectively.This one water molecule difference in the dominant cluster size may due to the nuclear quantum effects on water’s hydrogen bonded network.It is the first time to experimentally show the size distribution of water clusters over a wide range（n=1–30）for pure
基金This research was supported by the National Natural Science Foundation of China(21834001 and 61871183)Innovation Program of Shanghai Municipal Education Commission(2017-01-07-00-02-E00023).
文摘Membrane protein molecules can self-assemble to form a single-biomolecule interface,which can accommodate one single molecule at a time and provide a suitable sensing environment for single-molecule measurements.To achieve the high temporal and spatial resolution for revealing the heterogenous of single molecules,one of the most important challenge is to construct a functional single-biomolecule interface.
基金supported by the National Natural Science Foundation of China (21327807, 21421004)Innovation Program of Shanghai Municipal Education Commission (2017-01-07-00-02E00023)the Fundamental Research Funds for the Central Universities (222201718001, 222201717003)
文摘Nanopore is an ultra-sensitive electrochemical technique for single molecular detection in confined space. To suppress the noise in detection of the weak current of nanopore, we investigated the influence of membrane capacitance and applied voltage on the noise of the current signal by model analysis, simulation and experiment. The obtained results demonstrated that membrane capacitance affects the noise by amplifying the noise of the applied voltage. Therefore, suppression of applied voltage noise is an efficient approach for reducing the noise in nanopore detection. Here, we developed an ultra-low noise instrument system for detecting the single molecule signal in nanopores. As demonstrated by nanopore experiments, the p-p noise of the developed system during the recording is reduced to 3.2B pA using the filter of 5 kHz. Therefore, the developed system could be applied in highly sensitive nanopore detection.
基金funding from National Natural Science Foundation of China(21834001,21925403,21874070,21790390,21790391,61901171)sponsored by National Ten Thousand Talent Program for young topnotch talent,funding from the European Union’s Horizon 2020research and innovation programme under the Marie Skodowska-Curie grant agreement No 812398,funding supported by the Strategic Priority Research Program of Chinese Academy of Sciences(XDB30000000)+5 种基金the National Basic Research Program of China(2018YFE0200800,2018YFA0703501 and 2016YFA0200104)the Chinese Academy of Sciences(QYZDJSSW-SLH030)funding from Office of Naval Research(N00014-19-1-2331)the US Air Force Office of Scientific Research MURI(FA9550-14-1-0003)the Nanostructures for Electrical Energy Storage(NEES)an Energy Frontier Research Center funded by the US Department of Energy,Office of Science and Basic Energy Sciences under Award number DESC0001160,support from the Office of Naval Research DURIP program(N00014-18-1-2235)。
文摘Measurements at the single-entity level provide more precise diagnosis and understanding of basic biological and chemical processes.Recent advances in the chemical measurement provide a means for ultra-sensitive analysis.Confining the single analyte and electrons near the sensing interface can greatly enhance the sensitivity and selectivity.In this review,we summarize the recent progress in single-entity electrochemistry of single molecules,single particles,single cells and even brain analysis.The benefits of confining these entities to a compatible size sensing interface are exemplified.Finally,the opportunities and challenges of single entity electrochemistry are addressed.
基金This research was supported by the National Natural Science Foundation of China(Grant Nos.21906054,21922405 and 22027806)the Fundamental Research Funds for the Central Universities(No.14380239).
文摘Main observation and conclusion Single nanoparticle collision has attracted great attention in the last several years to reveal the electron transfer and motion trajectories of individual particles at the electrode surface.An envelope algorithm is proposed for further reading and demonstrating the corresponding current signals.
基金supported by the National Natural Science Foundation of China (61871183, 21834001)sponsored by National Ten Thousand Talent Program for young top-notch talent and Shanghai Rising-Star Program (19QA1402300)sponsored by the China Scholarship Council (201806740044)
文摘Nanopore techniques are experiencing a gallop since it walked out the notebook and show its charm on the science arena.The nanoscale pore offers a single-molecule resolution with a label-free and high-selective manner for the research of molecular structures,molecular dynamics,single-molecule reactions and for a variety of applications in biophysics and bionanotechnology.In this review,we introduce the construction of three types of nanopore platforms along with the latest progress in DNA sensing,structure and dynamics analysis of peptides/proteins,and the detection of redox reactions with new sensing mechanisms.Then,we depict nanopore data processing methods which provide an insight of data mining under the background ofbig data.We could fully expect the great impact of nanopore techniques on not only for DNA sequencing and sensing applications,but also in protein sequencing and clinical diagnostics.
基金This research was supported by the National Natural Science Foundation of China(21922405,21834001,and 61871183)Excellent Research Program of Nanjing University(ZYJH004)Yi-Lun Ying is sponsored by National Ten Thousand Talent Program for Young Top-Notch Talent.
文摘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,highthroughput,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 T4 oligonucleotide kinase(PNK)further achieved the nanopore evaluation of its phosphatase activity and real-time monitoring of its phosphatase-catalyzed dephosphorylation at a singlemolecule 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.
基金supported by the National Natural Science Foundation of China(nos.21822805,21908065,31871430,81802979,818800585,and 8180032537)Young Medical Talents Training Program of Shanghai(2018)+3 种基金the Commission of Science and Technology of Shanghai Municipality(no.18430711000)the Australian National Health and Medical Research Council(nos.APP1126091 and APP1125794)the Science and Technology Commission of Shanghai Municipality for the Shanghai International Cooperation Program(18430711000)the China Postdoctoral Science Foundation(nos.2019M651427 and 2020T130197),W.Yang acknowledges the financial support of the innovative research team of high-level local universities in Shanghai.
文摘Ratiometric probes facilitate quantitative studies via self-calibration and are cherished for bioimaging.Often,a small probe-product spectral separation leads to crosstalk,but the rational development of ratiometric probes with zero probe-product crosstalk remains challenging.Harnessing the recent progress on photophysical modulation of xanthenoid fluorochromes,we propose a powerful and versatile probe design principle,that is,“bridging-group modification,”and developed totalROX,a robust probe for monitoring the total cellular oxidative capacity.
