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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 ***,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 *** such as Anderson,Keggin,Dawson,and a few lacunary Dawson polyoxometalates with very similar structures,even with only a two-atom difference,could be *** nanopore device could simultaneously measure multiple nanoclusters in a mixture qualitatively and ***,molecular dynamics(MD)simulations provided microscopic understandings of the nanocluster translocation dynamics and yielded 2D dwell time–current blockage spectra in close agreement with *** nanopore platform provides a novel powerful tool for nanocluster characterization.

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

Evolution of Monkeypox C9L RNA G-Quadruplex Elevates the Translation of Its Only Kelch-like Protein by Accelerating G-Quadruplex Unfolding Kinetics

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CCS chemistry 2024年第4期6卷 953-963页

作者： Yicong Dai Xucong Teng Difei Hu Qiushuang Zhang Jinghong Li Department of chemistry Center for Bioanalytical ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyTsinghua UniversityBeijing 100084 New Cornerstone Science Laboratory Shenzhen 518054 Beijing Life Science Academy Beijing 102209 center for bioanalytical chemistry Hefei National Laboratory of Physical Sciences at the MicroscaleUniversity of Science and Technology of ChinaHefei 230026

Genomic surveillance of monkeypox virus(MPXV)is essential to explore the reason of its unusual *** phylogenomic analysis of the MPXV genome mainly focuses on the effect of amino acid ***,we explore the evolutionary variation of RNA G-quadruplex(RG4)of MPXV and find that the genome evolution of MPXV can also produce new effects through changes in the RG4 *** RG4 is located in MPXV’s only Kelch-like C9L gene,which encodes for an antagonist of the innate immune *** evolution of this virus increases the unfolding kinetic constant of C9L RG4 and promotes the C9 protein level in living ***,all reported MPXV genomes in 2022 carry the C9L-RG4-5 pattern with the highest unfolding kinetic ***,the RG4 ligand,RGB-1,can impede the unfolding of C9L-RG4-5 and thereby reduce the C9 protein *** findings carve out a new path to comprehensively understanding MPXV virology.

关键词： G-quadruplex RNA secondary structure unfolding kinetics monkeypox virus genomic evolution immune evasion

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

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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 *** covalent binding mode of the tetrapeptidic titrant was elucidated by the determination of the crystal structure of the enzyme–titrant *** fluorogenic substrates of M^(pro),including a prototypical,internally quenched Dabcyl-EDANS peptide,were compared in terms of solubility under typical assay *** 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

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 *** to their excellent catalytic characteristics,biocompatibility,and environmental favorability,carbondots-based(CDs) nanozymes have inspired a research ***,no review focusing on CDs nanozymes has been published,even though substantial advances have been ***,the advances,catalytic activities,and applications of CDs nanozymes are highlighted and *** addition,the critical issues and challenges of researching nanozymes are *** 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

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Recent advances in enzyme-free and enzyme-mediated single-nucleotide variation assay in vitro

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National Science Review 2024年第5期11卷 365-384页

作者： Erhu Xiong Pengfei Liu Ruijie Deng Kaixiang Zhang Ronghua Yang Jinghong Li Key Laboratory of Chemical Biology &Traditional Chinese Medicine Research Ministry of EducationCollege of Chemistry and Chemical Engineering Hunan Normal University College of Biomass Science and Engineering Healthy Food Evaluation Research CenterSichuan University School of Pharmaceutical Sciences Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases Zhengzhou University Department of chemistry Center for Bioanalytical Chemistry Key Laboratory of Bioorganic Phosphorus Chemistry& Chemical BiologyTsinghua University Beijing Institute of Life Science and Technology

Single-nucleotide variants(SNVs) are the most common type variation of sequence alterations at a specific location in the genome, thus involving significant clinical and biological information. The assay of SNVs has engaged great awareness, because many genome-wide association studies demonstrated that SNVs are highly associated with serious human diseases. Moreover, the investigation of SNV expression levels in single cells are capable of visualizing genetic information and revealing the complexity and heterogeneity of single-nucleotide mutation-related diseases. Thus, developing SNV assay approaches in vitro, particularly in single cells, is becoming increasingly in demand. In this review, we summarized recent progress in the enzyme-free and enzyme-mediated strategies enabling SNV assay transition from sensing interface to the test tube and single cells, which will potentially delve deeper into the knowledge of SNV functions and disease associations, as well as discovering new pathways to diagnose and treat diseases based on individual genetic profiles. The leap of SNV assay achievements will motivate observation and measurement genetic variations in single cells, even within living organisms, delve into the knowledge of SNV functions and disease associations, as well as open up entirely new avenues in the diagnosis and treatment of diseases based on individual genetic profiles.

关键词： single-nucleotide variant point mutation in vitro enzyme-free assay enzyme-mediated assay

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 ***,the intracellular fluorescence sensing of ATP using ATP aptamer remains difficult owing to non-target displacement and susceptibility toward enzymatic ***,by combining 2D Cu-MOF nanosheets and FAM labelled ATP aptamer,we developed a fluorescent Cu-MOFs/aptamer nanoprobe to image and sense intracellular *** nanoprobe reveals a very low fluorescence intensity because of the excellent quenching efficiency of 2D Cu-MOF *** presence of ATP was capable to dissociate the FAM-aptamer from Cu-MOF nanosheets and resulted in an intense fluorescence *** Cu-MOFs/aptamer nanoprobe enables highly sensitive and selective measurement of ATP level ranging from 10μM to 800μM with a detection limit of 4.24μ*** 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 *** 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

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Photosensitizer-assisted direct 2D patterning and 3D printing of colloidal quantum dots

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Nano Research 2024年第12期17卷 10460-10466页

作者： Wenyue Qing Yilong Si Mingfeng Cai Likuan Zhou Longjia Wu Zhengwei Hou Dan Liu Xiaoli Tian Wangyu Liu Linhan Lin Hao Zhang Department of chemistry Center for BioAnalytical ChemistryKey Laboratory of Bioorganic Phosphorus Chemistry&Chemical Biology(Ministry of Education)Tsinghua UniversityBeijing 100084China TCL Research Shenzhen 518067China Key Laboratory of Advanced Materials(MOE) School of Materials Science and EngineeringTsinghua UniversityBeijing 100084China State Key Laboratory of Precision Measurement Technology and Instruments Department of Precision InstrumentsTsinghua UniversityBeijing 100084China

Direct photopatterning is a powerful strategy for patterning colloidal quantum dots(QDs)for their integration in various electronic and optoelectronic ***,ultraviolet(UV)exposure required for QD patterning,especially those with short wavelength(e.g.,deep UV light),can degrade the photo-,and electroluminescence,and other properties of patterned *** we develop a photosensitizer-assisted approach for direct photopatterning of QDs with h-line(centered at 405 nm)UV light and better preservation of their luminescent *** approach uses a photosensitizer that can absorb the h-line UV light and transfer the energy to activate bisazide-based crosslinkers via Dexter energy ***,high-resolution(smallest feature size,2μm),and full-color patterns of red,green,and blue QD layers can be *** patterned QD layers maintain up to~90%of their original photoluminescent quantum yields,comparing favorably with those(<60%)of QDs patterned without *** further extended the strategy to the direct three-dimensional(3D)printing of *** photosensitizerassisted approach offers a new way for direct two-dimensional(2D)photopatterning and 3D printing of colloidal QDs,with implications in building high-performance QD optoelectronic devices.

关键词： direct photopatterning quantum dots photosensitizer Dexter energy transfer three-dimensional(3D)printing

Ferricyanide-Promoted Oxidative Activation and Ligation of Protein Thioacids in Neutral Aqueous Media

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CCS chemistry 2024年第8期6卷 2031-2043页

作者： Guo-Chao Chu Lu-Jun Liang Rui Zhao Yan-Yan Guo Chun-Tong Li Chong Zuo Huasong Ai Xiao Hua Zi-Chen Li Yi-Ming Li Lei Liu NewCornerstone Science Laboratory Tsinghua-Peking Center for Life SciencesMinistry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical BiologyCenter for Synthetic and Systems BiologyDepartment of ChemistryTsinghua UniversityBeijing 100084 School of Food and Biological Engineering Hefei University of TechnologyHefei 230009 center for bioanalytical chemistry Hefei National Laboratory of Physical Science at MicroscaleUniversity of Science and Technology of ChinaHefei 230026 Department of chemistry University of Science and Technology of ChinaHefei 230026

Ferricyanide-promoted oxidative activation of Nacylatedα-aminothioacids for amide bond formation withα-aminonitriles was recently shown to be a plausible pathway for prebiotic peptide *** we describe the finding that by adding sodium azide and thiols,ferricyanide oxidation can elicit highly efficient and clean conversion of fully unprotected peptide or protein thioacids in neutral aqueous media to the corresponding *** transformation enables the development of ferricyanide-promoted thioacid-based native chemical ligation(NCL)as a new redox-based method for chemical protein synthesis,which does not need to change pH and is therefore operationally easy for ligation at small *** effectiveness of the ferricyanide-promoted thioacid-based NCL was illustrated by synthesis of an ISG15-modified MDA5 segment under nondenaturing conditions and synthesis of an acetylated ubiquitin(Ub)-modified histone H2A through an N-to-C sequential *** work broadens the concept of on-demand oxidative activation strategy for protein ligation and provides a new useful supplement to the repertoire of methods for chemical protein synthesis,particularly for studies on proteins carrying Ub family modifications.

关键词： chemical protein synthesis protein thioacid ferricyanide oxidation native chemical ligation ubiquitin family modifications