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Real-time identification of multiple nanoclusters with a protein nanopore in single-cluster level

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Nano Research 2024年第1期17卷 262-269页

作者： Ling Zhang Peilei He Huang Chen Qingda Liu Libo Li Xun Wang Jinghong Li Department of chemistry Center for BioAnalytical ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry&Chemical BiologyTsinghua UniversityBeijing 100084China School of chemistry and Chemical Engineering Guangdong Prov Key Lab Green Chem Prod TechnolSouth China University of TechnologyGuangzhou 510640China New Cornerstone Science Laboratory Shenzhen 518054China Beijing Institute of Life Science and Technology Beijing 102206China center for bioanalytical chemistry Hefei National Laboratory of Physical Science at MicroscaleUniversity of Science and Technology of ChinaHefei 230026China

It is important and challenging to analyze nanocluster structure with atomic precision.Herein,α-hemolysin nanopore was used to identify nanoclusters at the single molecule level by providing two-dimensional(2D)dwell time–current blockage spectra and translocation event frequency which sensitively depended on their structures.Nanoclusters such as Anderson,Keggin,Dawson,and a few lacunary Dawson polyoxometalates with very similar structures,even with only a two-atom difference,could be discriminated.This nanopore device could simultaneously measure multiple nanoclusters in a mixture qualitatively and quantitatively.Furthermore,molecular dynamics(MD)simulations provided microscopic understandings of the nanocluster translocation dynamics and yielded 2D dwell time–current blockage spectra in close agreement with experiments.The nanopore platform provides a novel powerful tool for nanocluster characterization.

关键词： nanopore single-molecule nanocluster polyoxometalates real-time detection

Development of an active-site titrant for SARS-CoV-2 main protease as an indispensable tool for evaluating enzyme kinetics

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Acta Pharmaceutica Sinica B 2024年第5期14卷 2349-2357页

作者： Rabea Voget Julian Breidenbach Tobias Claff Alexandra Hingst Katharina Sylvester Christian Steinebach Lan Phuong Vu Renato H.Weiße Ulrike Bartz Norbert Sträter Christa E.Müller Michael Gütschow Pharmaceutical Institute Pharmaceutical&Medicinal ChemistryUniversity of BonnBonn 53121Germany Institute of bioanalytical chemistry Center for Biotechnology and BiomedicineLeipzig UniversityLeipzig 04103Germany Department of Natural Sciences University of Applied Sciences Bonn-Rhein-SiegRheinbach 53359Germany

A titrant for the SARS-CoV-2 main protease(M^(pro))was developed that enables,for the first time,the exact determination of the concentration of the enzymatically active M^(pro) by active-site titration.The covalent binding mode of the tetrapeptidic titrant was elucidated by the determination of the crystal structure of the enzyme–titrant complex.Four fluorogenic substrates of M^(pro),including a prototypical,internally quenched Dabcyl-EDANS peptide,were compared in terms of solubility under typical assay conditions.By exploiting the new titrant,key kinetic parameters for the M^(pro)-catalyzed cleavage of these substrates were determined.

关键词： COVID-19 SARS-CoV-2 Main protease Peptide nitriles Fluorogenic substrates Active-site titration X-ray crystallography Inner filter effect

吲哚-3-乙酸,阿尔茨海默病的潜在治疗靶点（英文）

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Science Bulletin 2024年第2期 146-147页

作者：李景虹 Department of chemistry Key Laboratory of Bioorganic Phosphorus chemistry and Chemical Biology (Ministry of Education) center for bioanalytical chemistry Tsinghua University

Alzheimer’s disease(AD) is a chronic and progressive neurodegenerative disease that is characterized by the presence of amyloid-β(Aβ) plaques, hyperphosphorylated microtubule-associated tau protein(p-tau) neurofibrillary tangles and neuronal degeneration. According to recent data, AD is the most common global cause of dementia in the elderly.

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Simultaneous capture of ISG15 conjugating and deconjugating enzymes using a semi-synthetic ISG15-Dha probe

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Science China chemistry 2023年第3期66卷 837-844页

作者： Chuntong Li Tian Wang Lujun Liang Guochao Chu Jiachen Zhang Wei He Lei Liu Jinghong Li Department of chemistry Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical BiologyCenter for Synthetic and Systems BiologyState Key Laboratory of Chemical Oncogenomics(Shenzhen)Tsinghua UniversityBeijing 100084China School of Pharmaceutical Sciences Tsinghua UniversityBeijing 100084China center for bioanalytical chemistry Hefei National Laboratory of Physical Science at MicroscaleUniversity of Science and Technology of ChinaHefei 230026China

ISG15 is a ubiquitin-like(Ubl) protein attached to substrate proteins by ISG15 conjugating enzymes whose dysregulation is implicated in a multitude of disease processes, but the probing of these enzymes remains to be accomplished. Here, we describe the development of a new activity-based probe ISG15-Dha(dehydroalanine) through protein semi-synthesis. In vitro crosslinking and cell lysate proteomic profiling experiments showed that this probe can sequentially capture ISG15 conjugating enzymes including E1 enzyme UBA7, E2 enzyme UBE2L6, E3 enzyme HERC5, the previously known ISG15 deconjugating enzyme(USP18), as well as some other enzymes(USP5 and USP14) which we additionally confirmed to impart deISGylation activity. Collectively, ISG15-Dha provides a new tool that can simultaneously capture ISG15 conjugating and deconjugating enzymes for biochemical or pharmacological studies.

关键词： ISG15-Dha probe semi-synthesis activity based probe proteomics ISGylation

Nanotechnology in bioanalytical chemistry

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Chemical Research in Chinese Universities 2024年第2期40卷 159-161页

作者： CHEN Chunying ZHAO Yuliang CAS Key Laboratory for Biomedical Effects of Nanomaterials&Nanosafety National Center for Nanoscience and TechnologyBeijing 100190P.R.China

With the increasing advances in bioanalytical chemistry,nanotechnology has become an important tool and key technology for improving the understanding of fundamental chemistry and biology fields.The ratio of surface area to volume of materials exponentially increases at the nanoscale,leading to the emergence of numerous novel physical and chemical phenomena.For instance,the surface energy of nanomaterials becomes significantly more pronounced compared to volume energy.

关键词： exponentially instance energy.

Extracellular Milieu and Membrane Receptor Dual-Driven DNA Nanorobot for Accurate in Vivo Tumor Imaging

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CCS chemistry 2022年第5期4卷 1597-1609页

作者： Kun Yuan Hong-Min Meng Yanan Wu Juan Chen Hui Xu Lingbo Qu Lele Li Zhaohui Li College of chemistry Green Catalysis CenterHenan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical ApplicationsZhengzhou Key Laboratory of Functional Nanomaterial and Medical TheranosticZhengzhou UniversityZhengzhou 450001 CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS center for Excellence in Nanoscience National Center for Nanoscience and TechnologyBeijing 100190

Precise diagnostic approaches have great potential in cancer intervention and prognosis.Although diverse DNA nanoprobes have been reported for tumor diagnosis,precise tumor imaging in vivo still encounters a great challenge due to the scarcity of exquisite design methodology.Herein,by assembling three programmable modules on a DNA triangular prism,we engineered a DNA nanorobot for simultaneous recognition of extracellular pH and cancer cell membrane receptor in an intelligent manner.Since the design uses two heterogeneous types of biomarkers as inputs,pH-RE not only could discriminate target tumor cells from similar cell mixtures with a recognition accuracy as high as 98.8%,but also could perform precise tumor imaging in living mice by intravenous injection.We expect that this extracellular pH and membrane receptor dual-driven DNA nanorobot will facilitate the establishment of a novel design paradigm for precise cancer diagnosis and therapy.

关键词： accurate cancer diagnosis DNA nanorobot in vivo tumor imaging logic gate pH_(e)and membrane receptors

Metabolic state oscillations in cerebral nuclei detected using two-photon fluorescence lifetime imaging microscopy

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Chinese Chemical Letters 2023年第1期34卷 300-303页

作者： Peng Zhou Jiawei Shen Jun Liang Tian Xue Yuansheng Sun Longhua Zhang Changlin Tian High Magnetic Field Laboratory Hefei Institutes of Physical ScienceChinese Academy of SciencesHefei 230031China The First Affiliated Hospital of USTC Division of Life Sciences and Medicineand Center for BioAnalytical ChemistryUniversity of Science and Technology of ChinaHefei 230026China ISS Inc.ChampaignIL 61822United States

The fluorescence lifetime of nicotinamide adenine dinucleotide(NADH),a key endogenous coenzyme and metabolic biomarker,can reflect the metabolic state of cells.To implement metabolic imaging of brain tissue at high resolution,we assembled a two-photon fluorescence lifetime imaging microscopy(FLIM)platform and verified the feasibility and stability of NADH-based two-photon FLIM in paraformaldehydefixed mouse cerebral slices.Furthermore,NADH based metabolic state oscillation was observed in cerebral nuclei suprachiasmatic nucleus(SCN).The free NADH fraction displayed a relatively lower level in the daytime than at the onset of night,and an ultradian oscillation at night was observed.Through the combination of high-resolution imaging and immunostaining data,the metabolic tendency of different cell types was detected after the first two hours of the day and at night.Thus,two-photon FLIM analysis of NADH in paraformaldehyde-fixed cerebral slices provides a high-resolution and label-free method to explore the metabolic state of deep brain regions.

关键词： NADH Fluorescence lifetime imaging microscopy Brain metabolism Metabolic oscillation High resolution

Two-Dimension(2D) Cu-MOFs/aptamer Nanoprobe for In Situ ATP Imaging in Living Cells

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Journal of Analysis and Testing 2021年第2期5卷 165-173页

作者： Xinxin Shi Hui Xu Yanan Wu Yanmin Zhao Hong-Min Meng Zhaohui Li Lingbo Qu College of chemistry Green Catalysis CenterHenan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical ApplicationsZhengzhou Key Laboratory of Functional Nanomaterial and Medical TheranosticZhengzhou UniversityZhengzhou 450001China

Monitoring the intracellular adenosine triphosphate(ATP)level is vital for elaborating its function in physiological states.However,the intracellular fluorescence sensing of ATP using ATP aptamer remains difficult owing to non-target displacement and susceptibility toward enzymatic degradation.Herein,by combining 2D Cu-MOF nanosheets and FAM labelled ATP aptamer,we developed a fluorescent Cu-MOFs/aptamer nanoprobe to image and sense intracellular ATP.This nanoprobe reveals a very low fluorescence intensity because of the excellent quenching efficiency of 2D Cu-MOF nanosheets.The presence of ATP was capable to dissociate the FAM-aptamer from Cu-MOF nanosheets and resulted in an intense fluorescence signal.The Cu-MOFs/aptamer nanoprobe enables highly sensitive and selective measurement of ATP level ranging from 10μM to 800μM with a detection limit of 4.24μM.This nanosystem also further realized in situ detection of the undulation of ATP trigged by drug stimulation,depending on the selective delivery of the nanoprobe and attractive capability of resisting nonspecific displacement.The constructed nanoprobe may supply a potential platform in clinical diagnostics and biological studies.

关键词： Metal–organic frameworks Aptamer ATP Bio-sensing Cell imaging

Recent progress in carbon-dots-based nanozymes for chemosensing and biomedical applications

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Chinese Chemical Letters 2021年第10期32卷 2994-3006页

作者： Deming He Minmin Yan Pengjuan Sun Yuanqiang Sun Lingbo Qu Zhaohui Li College of chemistry Green Catalysis CenterHenan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical ApplicationsZhengzhou Key Laboratory of Functional Nanomaterial and Medical TheranosticZhengzhou UniversityZhengzhou 450001China

Nanozymes are nanomaterials with enzyme-like activities that efficiently overcome the drawbacks of natural enzymes in biosensing,detection,and biomedical fields,and they are the most widely used artificial enzymes.Owing to their excellent catalytic characteristics,biocompatibility,and environmental favorability,carbondots-based(CDs) nanozymes have inspired a research upsurge.However,no review focusing on CDs nanozymes has been published,even though substantial advances have been achieved.Herein,the advances,catalytic activities,and applications of CDs nanozymes are highlighted and summarized.In addition,the critical issues and challenges of researching nanozymes are discussed.We hope that this review will broaden the horizons of nanozymes and CDs nanozymes,as well as promote their development.

关键词： Carbon dots Nanozyme Chemosensing Catalytic activity Bioimaging