Current protocols in chemical biology最新文献_第9页

Tracking the Activity of mTORC1 in Living Cells Using Genetically Encoded FRET-based Biosensor TORCAR 利用基因编码的基于fret的生物传感器TORCAR跟踪活细胞中mTORC1的活性

Current protocols in chemical biology Pub Date : 2016-12-07 DOI: 10.1002/cpch.11

Xin Zhou, Simin Li, Jin Zhang

引用次数: 7

Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging 循环免疫荧光(CycIF)，一种高度复用的单细胞成像方法

Current protocols in chemical biology Pub Date : 2016-12-07 DOI: 10.1002/cpch.14

Jia-Ren Lin, Mohammad Fallahi-Sichani, Jia-Yun Chen, Peter K. Sorger

{"title":"Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging","authors":"Jia-Ren Lin, Mohammad Fallahi-Sichani, Jia-Yun Chen, Peter K. Sorger","doi":"10.1002/cpch.14","DOIUrl":"10.1002/cpch.14","url":null,"abstract":"\u0000 Cyclic Immunofluorescence (CycIF) is a public-domain method for performing highly multiplexed immunofluorescence imaging using a conventional epifluorescence microscope. It uses simple reagents and existing antibodies to construct images with up to 30 channels by sequential 4- to 6-channel imaging followed by fluorophore inactivation. Three variant methods are described, the most generally useful of which involves staining fixed cells with antibodies directly conjugated to Alexa Fluor dyes and imaging in four colors, inactivating fluorophores using a mild base in the presence of hydrogen peroxide and light, and then performing another round of staining and imaging. Cell morphology is preserved through multiple rounds of CycIF, and signal-to-noise ratios appear to increase. Unlike antibody-stripping methods, CycIF is gentle and optimized for monolayers of cultured cells. A second protocol involves indirect immunofluorescence and a third enables chemical inactivation of genetically encoded fluorescent proteins, allowing multiplex immunofluorescence to be combined with live-cell analysis of cells expressing fluorescent reporter proteins. © 2016 by John Wiley & Sons, Inc.","PeriodicalId":38051,"journal":{"name":"Current protocols in chemical biology","volume":"8 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpch.14","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50803186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 121

Nanoparticle-Templated Molecular Recognition Platforms for Detection of Biological Analytes 用于生物分析物检测的纳米颗粒模板分子识别平台

Current protocols in chemical biology Pub Date : 2016-09-13 DOI: 10.1002/cpch.10

Abraham G. Beyene, Gozde S. Demirer, Markita P. Landry

{"title":"Nanoparticle-Templated Molecular Recognition Platforms for Detection of Biological Analytes","authors":"Abraham G. Beyene, Gozde S. Demirer, Markita P. Landry","doi":"10.1002/cpch.10","DOIUrl":"10.1002/cpch.10","url":null,"abstract":"Molecular recognition of biological analytes with optical nanosensors provides both spatial and temporal biochemical information. A recently developed sensing platform exploits near-infrared fluorescent single-wall carbon nanotubes combined with electrostatically pinned heteropolymers to yield a synthetic molecular recognition technique that is maximally transparent through biological matter. This molecular recognition technique is known as corona phase molecular recognition (CoPhMoRe). In CoPhMoRe, the specificity of a folded polymer toward an analyte does not arise from a pre-existing polymer-analyte chemical affinity. Rather, specificity is conferred through conformational changes undergone by a polymer that is pinned to the surface of a nanoparticle in the presence of an analyte and the subsequent modifications in fluorescence readout of the nanoparticles. The protocols in this article describe a novel single-molecule microscopy tool (near-infrared fluorescence and total internal reflection fluorescence [nIRF TIRF] hybrid microscope) to visualize the CoPhMoRe recognition process, enabling a better understanding of synthetic molecular recognition. We describe this requisite microscope for simultaneous single-molecule visualization of optical molecular recognition and signal transduction. We elaborate on the general procedures for synthesizing and identifying single-walled carbon nanotube-based sensors that employ CoPhMoRe via two biologically relevant examples of single-molecule recognition for the hormone estradiol and the neurotransmitter dopamine. © 2016 by John Wiley & Sons, Inc.","PeriodicalId":38051,"journal":{"name":"Current protocols in chemical biology","volume":"8 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpch.10","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9756994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 24

Reverse Phase Protein Arrays for Compound Profiling 用于化合物分析的反相蛋白质阵列

Current protocols in chemical biology Pub Date : 2016-09-13 DOI: 10.1002/cpch.9

Nathan Moerke, Mohammad Fallahi-Sichani

引用次数: 2

Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC) dna程序化细胞组装(DPAC)制备三维重组类器官阵列

Current protocols in chemical biology Pub Date : 2016-09-13 DOI: 10.1002/cpch.8

Michael E. Todhunter, Robert J. Weber, Justin Farlow, Noel Y. Jee, Alec E. Cerchiari, Zev J. Gartner

{"title":"Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC)","authors":"Michael E. Todhunter, Robert J. Weber, Justin Farlow, Noel Y. Jee, Alec E. Cerchiari, Zev J. Gartner","doi":"10.1002/cpch.8","DOIUrl":"10.1002/cpch.8","url":null,"abstract":"Tissues are the organizational units of function in metazoan organisms. Tissues comprise an assortment of cellular building blocks, soluble factors, and extracellular matrix (ECM) composed into specific three-dimensional (3-D) structures. The capacity to reconstitute tissues in vitro with the structural complexity observed in vivo is key to understanding processes such as morphogenesis, homeostasis, and disease. In this article, we describe DNA-programmed assembly of cells (DPAC), a method to fabricate viable, functional arrays of organoid-like tissues within 3-D ECM gels. In DPAC, dissociated cells are chemically functionalized with degradable oligonucleotide “Velcro,” allowing rapid, specific, and reversible cell adhesion to a two-dimensional (2-D) template patterned with complementary DNA. An iterative assembly process builds up organoids, layer-by-layer, from this initial 2-D template and into the third dimension. Cleavage of the DNA releases the completed array of tissues that are captured and fully embedded in ECM gels for culture and observation. DPAC controls the size, shape, composition, and spatial heterogeneity of organoids and permits positioning of constituent cells with single-cell resolution even within cultures several centimeters long. © 2016 by John Wiley & Sons, Inc.","PeriodicalId":38051,"journal":{"name":"Current protocols in chemical biology","volume":"8 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpch.8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50803240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Combinatorial Library Screening Coupled to Mass Spectrometry to Identify Valuable Cyclic Peptides 组合文库筛选与质谱联用鉴定有价值的环状肽

Current protocols in chemical biology Pub Date : 2016-06-02 DOI: 10.1002/cpch.2

Silvia A. Camperi, Silvana L. Giudicessi, María C. Martínez-Ceron, Juan M. Gurevich-Messina, Soledad L. Saavedra, Gerardo Acosta, Osvaldo Cascone, Rosa Erra-Balsells, Fernando Albericio

{"title":"Combinatorial Library Screening Coupled to Mass Spectrometry to Identify Valuable Cyclic Peptides","authors":"Silvia A. Camperi, Silvana L. Giudicessi, María C. Martínez-Ceron, Juan M. Gurevich-Messina, Soledad L. Saavedra, Gerardo Acosta, Osvaldo Cascone, Rosa Erra-Balsells, Fernando Albericio","doi":"10.1002/cpch.2","DOIUrl":"10.1002/cpch.2","url":null,"abstract":"Combinatorial library screening coupled to mass spectrometry (MS) analysis is a practical approach to identify useful peptides. Cyclic peptides can have high biological activity, selectivity, and affinity for target proteins, and high stability against proteolytic degradation. Here we describe two strategies to prepare combinatorial libraries suitable for MS analysis to accelerate the discovery of cyclic peptide structures. Both approaches use ChemMatrix resin and the linker 4‐hydroxymethylbenzoic acid. One strategy involves the synthesis of a one‐bead–two‐peptides library in which each bead contains both the cyclic peptide and its linear counterpart to facilitate MS analysis. The other protocol is based on the synthesis of a cyclic depsipeptide library in which a glycolamidic ester group is incorporated by adding glycolic acid. After library screening, the ring is opened and the peptide is released simultaneously for subsequent MS analysis. © 2016 by John Wiley & Sons, Inc.","PeriodicalId":38051,"journal":{"name":"Current protocols in chemical biology","volume":"8 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpch.2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34447499","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Optogenetic Control of Nuclear Protein Import in Living Cells Using Light-Inducible Nuclear Localization Signals (LINuS) 利用光诱导核定位信号(LINuS)光遗传学控制活细胞核蛋白输入

Current protocols in chemical biology Pub Date : 2016-06-02 DOI: 10.1002/cpch.4

Pierre Wehler, Dominik Niopek, Roland Eils, Barbara Di Ventura

引用次数: 12

Liquid Exfoliation of Layered Transition Metal Dichalcogenides for Biological Applications 层状过渡金属二硫族化合物的液体剥离及其生物应用

Current protocols in chemical biology Pub Date : 2016-06-02 DOI: 10.1002/cpch.3

Emily P. Nguyen, Torben Daeneke, Serge Zhuiykov, Kourosh Kalantar-zadeh

引用次数: 18

Pseudo-Ligandless Click Chemistry for Oligonucleotide Conjugation 寡核苷酸偶联的伪无配体点击化学

Current protocols in chemical biology Pub Date : 2016-06-02 DOI: 10.1002/cpch.1

Stephanie Mack, Munira F. Fouz, Sourav K. Dey, Subha R. Das

引用次数: 6

Hollow-Fiber Methodology for Pharmacokinetic/Pharmacodynamic Studies of Antimalarial Compounds 抗疟化合物药动学/药效学研究的中空纤维方法学

Current protocols in chemical biology Pub Date : 2016-03-16 DOI: 10.1002/9780470559277.ch150194

Emily Caton, Elizabeth Nenortas, Rahul P. Bakshi, Theresa A. Shapiro

引用次数: 5