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Optical approaches in study of nanocatalysis with single-molecule and single-particle resolution

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Frontiers of Optoelectronics 2015年第4期8卷 379-393页

作者： Kun LI Weiwei QIN Yan XU Tianhuan PENG Di LI division of physical biology & bioimaging center Shanghai Synchrotron Radiation Facility Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China

Studying the activity of individual nanocata- lysts, especially with high spatiotemporal resolution of single-molecule and single-turnover scale, is essential for the understanding of catalytic mechanism and the designing of effective catalysts. Several approaches have been developed to monitor the catalytic reaction on single catalysts. In this review, we summarized the updated progresses of several new spectroscopic and microscopic approaches, including single-molecule fluorescence microscopy, surface-enhanced Raman spectroscopy, surface plasmon resonance microscopy and X-ray microscopy, for the study of single-molecule and single-particle catalysis.

关键词： nanocatalysis single-molecule fluorescence,surface-enhanced Raman localized surface plasmon reso-nance X-ray

Self-assembly of Micrometer-long DNA Nanoribbons with Four Oligonucleotides

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中国化学:英文版 2015年第5期33卷 522-526页

作者： Jie Chao Xiangyuan Ouyang Hongzhen Peng Shao Su Lianhui Wang Key Laboratory for Organic Electronics and Information Displays&Institute of Advanced Materials(IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials(SICAM)Nanjing University of Posts&TelecommunicationsNanjingJiangsu 210023China division of physical biology and Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai 201800China

DNA nanostructures have found widespread applications in areas including nanoelectronics and ***,traditional DNA origami needs a long single-stranded virus DNA and hundreds of short DNA strands,which make this method complicated and ***,we present a protocol for the assembly of DNA nanoribbons with only four *** nanoribbons with different dimensions were successfully assembled with a 96-base scafford strand and three short *** biotinylated nanoribbons could also be decorated with *** approach suggests that there exist great design spaces for the creation of simple nucleic acid nanostructures which could facilitate their application in plasmonic or drug delivery.

关键词： self-assembly DNA origami nanoribbons

Expression and radiolabeling of Cas9 protein

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Nuclear Science and Techniques 2017年第1期28卷 74-79页

作者： Qing-Long Yan Hua-Ting Kong Kai Xia Yu Zhang Ali Aladlbahi Ji-Ye Shi Li-Hua Wang Chun-Hai Fan Yun Zhao Ying Zhu Key Laboratory of Bio-Resources and Eco-Environment Ministry of Education College of Life Sciences Sichuan University Chengdu 610064 China division of physical biology and bioimaging center CAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied Physics Chinese Academy of Sciences Jiading Campus Shanghai 201800 China Chemistry Department King Saud University Riyadh 11451Saudi Arabia UCB Pharma Slough SL1 3WE UK

As a robust platform for genome editing,CRISPR/Cas9 is currently being explored for engineering biology or therapeutics,yet means for quantitative detection of Cas9 proteins remain to be fully ***,we expressed Cas9 proteins and developed a novel detection method that traced Cas9 based on radiolabeled *** optimizing the reaction conditions of reaction time,temperature and cycles,we obtained ^(125)I-Cas9 of high labeling *** prepared ^(125)I-Cas9 was stable in various media and preserved excellent genome editing ***,our strategy provides a convenient and efficient tool for further tracing biological behaviors of Cas9 proteins in living systems.

关键词： Cas9 Radiolabeling 125I labeling yield Stability

Superresolution imaging of DNA tetrahedral nanostructures in cells by STED method with continuous wave lasers

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Chinese Optics Letters 2014年第4期12卷 35-38页

作者：杜建聪邓素辉侯尚国乔玲玲陈建芳黄庆樊春海程亚赵云 College of Life Sciences SiChuan University division of physical biology and bioimaging center Shanghai Synchrotron Radiation FacilityShanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai Institute of Optics and Fine Mechanics Chinese Academy of Sciences

DNA tetrahedral nanostructures are considered to be uew nanocarriers because they can be precisely controlled and hold excellent penetration ability to the cellular membrane. Although the DNA tetrahedral nanostructure is extensively studied in biology and medicine, its behavior in the cells with nanoscale resolution is not understood clearly. In this letter, we demonstrate superrcsolution fluorescence imaging of the distribution of DNA tetrahedral nanostructures in the cell with a simulated emission depletion （STED） microscope, which is built based on a conventional eonfocal microscope and can t）rovide a resolution of 70 nm.

关键词： STED cell Superresolution imaging of DNA tetrahedral nanostructures in cells by STED method with continuous wave lasers DNA

Quantum dots protect against MPP＋-induced neurotoxicity in a cell model of Parkinson＇s disease through autophagy induction

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Science China Chemistry 2016年第11期59卷 1486-1491页

作者： Lu Wang Xiaoming Li Yuping Han Ting Wang Yun Zhao Aldalbahi Ali Nahed Nasser El-Sayed Jiye Shi Wenfeng Wang Chunhai Fan Nan Chen division of physical biology and bioimaging center Shanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of SciencesShanghai 201800China School of Life Science Sichuan UniversityChengdu 610064China Chemistry Department King Saud UniversityRiyadh 11451Saudi Arabia School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China UCB Pharma SloughSL1 3WEUK

Autophagy is a basic cellular process that decomposes damaged organelles and aberrant proteins. Dysregulation of autophagy is implicated in pathogenesis of neurodegenerative disorders, including Parkinson's disease(PD). Pharmacological compounds that stimulate autophagy can provide neuroprotection in models of PD. Nanoparticles have emerged as regulators of autophagy and have been tested in adjuvant therapy for diseases. In this present study, we explore the effects of quantum dots(QDs) that can induce autophagy in a cellular model of Parkinson's disease. Cd Te/Cd S/Zn S QDs protect differentiated rat pheochromocytoma PC12 cells from MPP+-induced cell damage, including reduced viability, apoptosis and accumulation of α-Synuclein, a characteristic protein of PD. The protective function of QDs is autophagy-dependent. In addition, we investigate the interaction between quantum dots and autophagic pathways and identify beclin1 as an essential factor for QDs-induced autophagy. Our results reveal new promise of QDs in the theranostic of neurodegenerative diseases.

关键词： quantum dots autophagy Parkinson’s disease α-Synuclein Beclin1

Genetically encoded X-ray cellular imaging for nanoscale protein localization

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National Science Review 2020年第7期7卷 1218-1227页

作者： Huating Kong Jichao Zhang Jiang Li Jian Wang Hyun-Joon Shin Renzhong Tai Qinglong Yan Kai Xia Jun Hu Lihua Wang Ying Zhu Chunhai Fan bioimaging center Shanghai Synchrotron Radiation FacilityZhangjiang Laboratory Shanghai Advanced Research Institute Chinese Academy of Sciences division of physical biology CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Canadian Light Source Inc. University of Saskatchewan Pohang Accelerator Laboratory POSTECH School of Chemistry and Chemical Engineering Frontiers Science Center for Transformative Molecules and Shanghai Key Laboratory for Nucleic Acids Chemistry and NanomedicineInstitute of Molecular Medicine Renji Hospital School of Medicine Shanghai Jiao Tong University

Spatial resolution defines the physical limit of microscopes for probing biomolecular localization and interactions in cells. Whereas synchrotron-based X-ray microscopy(XRM) represents a unique approach for imaging a whole cell with nanoscale resolution due to its intrinsic nanoscale resolution and great penetration ability, existing approaches to label biomolecules rely on the use of exogenous tags that are multi-step and error-prone. Here, we repurpose engineered peroxidases as genetically encoded X-ray-sensitive tags(GXET) for site-specific labeling of protein-of-interest in mammalian cells. We find that 3,3-diaminobenzidine(DAB) polymers that are in-situ catalytically formed by fusion-expressed peroxidases are visible under XRM. Using this new tag, we imaged the protein location associated with the alteration of a DNA-methylation pathway with an ultra-high resolution of 30 nanometers. Importantly, the excellent energy resolution of XRM enables multicolor imaging using different peroxidase tags. The development of GXET enlightens the way to nanoscopic imaging for biological studies.

关键词： synchrotron-based X-ray microscopy cellular imaging nanoscale protein localization genetically encoded X-ray tags 3,3-diaminobenzidine polymers

Asymmetric transportation induced by thermal noise at the nanoscale

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Science China(Physics,Mechanics & Astronomy) 2012年第5期55卷 751-756页

作者： WAN RongZheng HU Jun FANG HaiPing division of lnterfacial Water and Laboratory of physical biology Shanghai Institute of Applied PhysicsChinese Academy of SciencesP.O.Box 800-204Shanghai 201800China

Based on a simple model, we theoretically show that asymmetric transportation is possible in nanoscale systems experiencing thermal noise without the presence of extemal fluctuations. The key to this theoretical advance is that the correlation lengths of the thermal fluctuations become significantly long for nanoscale systems. This differs from macroscopic systems in which the thermal noises are usually treated as white noise. Our observation does not violate the second law of thermodynamics, since at the nanoscale, extra energy is required to keep the asymmetric structure against thermal fluctuations.

关键词： ratchet nanoscale thermal fluctuations

Effect of concentration and adsorption time on the formation of a large-scale origami pattern

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Nuclear Science and Techniques 2019年第7期30卷 62-67页

作者： Wen-Jing Liu Ping Zhang Tong Sun Lin Li Yu-Hui Wei Kai-Zhe Wang Lin Liu Bin Li division of physical biology and bioimaging Centre Shanghai Synchrotron Radiation Facility CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai 201800 China University of Chinese Academy of Sciences Beijing 100049 China Shanghai Advanced Research Institute Chinese Academy of Sciences Shanghai 201204 China School of Science Ningbo University Ningbo 315211 China

The arrangement of DNA-based nanostructures into the desired large-scale periodic pattern with the highest possible accuracy and control is essential for the DNA application in functional biomaterials;however, formation of a DNA nanostructure pattern without utilizing the molecular interactions in nanotechnology field remains difficult. In this article, we use the optimal concentration and adsorption time of origami to induce DNA origami in the form of a large-scale 2D pattern on mica without changing the origami itself. DNA origami structures can form a pattern by close packing of symmetric and electrostatic interactions between ions, which was confirmed by the atomic force microscopy images. Furthermore, we identified favorable conditions for the concentration of enable pattern formation with DNA origami. This work provides an insight to understand the adsorption of DNA on mica and guides researches on regular DNA nanostructure pattern, which can serve as templates for pattern formation of proteins or other biomolecules.

关键词： DNA Origami Pattern Atomic force microscopy Close packing

Probing the growth and mechanical properties of Bacillus subtilis biofilms through genetic mutation strategies

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Synthetic and Systems Biotechnology 2022年第3期7卷 965-971页

作者： Suying Liu Jiaofang Huang Chen Zhang Lihua Wang Chunhai Fan Chao Zhong division of physical biology and bioimaging center Shanghai Institute of Applied PhysicsChinese Academy of SciencesShanghaiChina University of Chinese Academy of Sciences BeijingChina School of physical Science and Technology ShanghaiTech UniversityShanghaiChina State Key Laboratory of Bioreactor Engineering East China University of Science and TechnologyShanghaiChina Institute of Physics Swiss Federal Institute of Technology Lausanne(EPFL)LausanneSwitzerland The Interdisciplinary Research center Shanghai Advanced Research InstituteChinese Academy of SciencesZhangjiang LaboratoryShanghaiChina School of Chemistry and Chemical Engineering Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghaiChina center for Materials Synthetic biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina CAS Key Laboratory of Quantitative Engineering biology Shenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina

Bacterial communities form biofilms on various surfaces by synthesizing a cohesive and protective extracellular matrix,and these biofilms protect microorganisms against harsh environmental *** subtilis is a widely used experimental species,and its biofilms are used as representative models of beneficial ***,*** biofilms are known to be rich in extracellular polymeric substances(EPS)and other biopolymers such as DNA and proteins like the amyloid protein TasA and the hydrophobic protein *** materials,which form an interconnected,cohesive,three-dimensional polymer network,provide the mechanical stability of biofilms and mediate their adherence to surfaces among other functional ***,we explored how genetically-encoded components specifically contribute to regulate the growth status,mechanical properties,and antibiotic resistance of *** biofilms,thereby establishing a solid empirical basis for understanding how various genetic engineering efforts are likely to affect the structure and function of *** noted discrete contributions to biofilm morphology,mechanical properties,and survival from major biofilm components such as EPS,TasA and *** example,EPS plays an important role in maintaining the stability of the mechanical properties and the antibiotic resistance of biofilms,whereas BslA has a significant impact on the resolution that can be obtained for printing *** work provides a deeper understanding of the internal interactions of biofilm components through systematic genetic *** thus not only broadens the application prospects of beneficial biofilms,but also serves as the basis of future strategies for targeting and effectively removing harmful biofilms.

关键词： Bacillus subtilis Biofilms Synthetic biology Living materials Environmental tolerance