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  • 1
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    Dynamics of nucleosome remodelling by individual ACF complexes (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-12-25
    Description: The ATP-dependent chromatin assembly and remodelling factor (ACF) functions to generate regularly spaced nucleosomes, which are required for heritable gene silencing. The mechanism by which ACF mobilizes nucleosomes remains poorly understood. Here we report a single-molecule FRET study that monitors the remodelling of individual nucleosomes by ACF in real time, revealing previously unknown remodelling intermediates and dynamics. In the presence of ACF and ATP, the nucleosomes exhibit gradual translocation along DNA interrupted by well-defined kinetic pauses that occurred after approximately seven or three to four base pairs of translocation. The binding of ACF, translocation of DNA and exiting of translocation pauses are all ATP-dependent, revealing three distinct functional roles of ATP during remodelling. At equilibrium, a continuously bound ACF complex can move the nucleosome back-and-forth many times before dissociation, indicating that ACF is a highly processive and bidirectional nucleosome translocase.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835771/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835771/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blosser, Timothy R -- Yang, Janet G -- Stone, Michael D -- Narlikar, Geeta J -- Zhuang, Xiaowei -- GM073767/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Dec 24;462(7276):1022-7. doi: 10.1038/nature08627.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Massachusetts 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033040" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; *Chromatin Assembly and Disassembly ; Fluorescence Resonance Energy Transfer ; Humans ; *Models, Molecular ; Nucleosomes/*chemistry ; Protein Structure, Tertiary ; Transcription Factors/*chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Multicolor super-resolution imaging with photo-switchable fluorescent probes (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-19
    Description: Recent advances in far-field optical nanoscopy have enabled fluorescence imaging with a spatial resolution of 20 to 50 nanometers. Multicolor super-resolution imaging, however, remains a challenging task. Here, we introduce a family of photo-switchable fluorescent probes and demonstrate multicolor stochastic optical reconstruction microscopy (STORM). Each probe consists of a photo-switchable "reporter" fluorophore that can be cycled between fluorescent and dark states, and an "activator" that facilitates photo-activation of the reporter. Combinatorial pairing of reporters and activators allows the creation of probes with many distinct colors. Iterative, color-specific activation of sparse subsets of these probes allows their localization with nanometer accuracy, enabling the construction of a super-resolution STORM image. Using this approach, we demonstrate multicolor imaging of DNA model samples and mammalian cells with 20- to 30-nanometer resolution. This technique will facilitate direct visualization of molecular interactions at the nanometer scale.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633025/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2633025/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bates, Mark -- Huang, Bo -- Dempsey, Graham T -- Zhuang, Xiaowei -- GM 068518/GM/NIGMS NIH HHS/ -- R01 GM068518/GM/NIGMS NIH HHS/ -- R01 GM068518-05/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1749-53. Epub 2007 Aug 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702910" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cercopithecus aethiops ; Clathrin-Coated Vesicles ; DNA/*analysis ; *DNA Probes ; *Fluorescent Dyes ; Microscopy, Fluorescence/methods ; Microtubules ; Nanotechnology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Chromosome organization by a nucleoid-associated protein in live bacteria (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-09-10
    Description: Bacterial chromosomes are confined in submicrometer-sized nucleoids. Chromosome organization is facilitated by nucleoid-associated proteins (NAPs), but the mechanisms of action remain elusive. In this work, we used super-resolution fluorescence microscopy, in combination with a chromosome-conformation capture assay, to study the distributions of major NAPs in live Escherichia coli cells. Four NAPs--HU, Fis, IHF, and StpA--were largely scattered throughout the nucleoid. In contrast, H-NS, a global transcriptional silencer, formed two compact clusters per chromosome, driven by oligomerization of DNA-bound H-NS through interactions mediated by the amino-terminal domain of the protein. H-NS sequestered the regulated operons into these clusters and juxtaposed numerous DNA segments broadly distributed throughout the chromosome. Deleting H-NS led to substantial chromosome reorganization. These observations demonstrate that H-NS plays a key role in global chromosome organization in bacteria.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329943/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329943/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Wenqin -- Li, Gene-Wei -- Chen, Chongyi -- Xie, X Sunney -- Zhuang, Xiaowei -- GM 096450/GM/NIGMS NIH HHS/ -- R01 GM096450/GM/NIGMS NIH HHS/ -- R01 GM096450-03/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Sep 9;333(6048):1445-9. doi: 10.1126/science.1204697.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21903814" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Division ; Chromosomes, Bacterial/*metabolism/*ultrastructure ; DNA, Bacterial/chemistry/*metabolism ; DNA-Binding Proteins/metabolism ; Escherichia coli K12/genetics/metabolism/*ultrastructure ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Factor For Inversion Stimulation Protein/metabolism ; Fimbriae Proteins/chemistry/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; Genetic Loci ; Genome, Bacterial ; Integration Host Factors/metabolism ; Molecular Chaperones/metabolism ; Nucleic Acid Conformation ; Operon ; Protein Multimerization ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-12-15
    Description: Actin and spectrin play important roles in neurons, but their organization in axons and dendrites remains unclear. We used stochastic optical reconstruction microscopy to study the organization of actin, spectrin, and associated proteins in neurons. Actin formed ringlike structures that wrapped around the circumference of axons and were evenly spaced along axonal shafts with a periodicity of ~180 to 190 nanometers. This periodic structure was not observed in dendrites, which instead contained long actin filaments running along dendritic shafts. Adducin, an actin-capping protein, colocalized with the actin rings. Spectrin exhibited periodic structures alternating with those of actin and adducin, and the distance between adjacent actin-adducin rings was comparable to the length of a spectrin tetramer. Sodium channels in axons were distributed in a periodic pattern coordinated with the underlying actin-spectrin-based cytoskeleton.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815867/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815867/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xu, Ke -- Zhong, Guisheng -- Zhuang, Xiaowei -- R01 GM096450/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2013 Jan 25;339(6118):452-6. doi: 10.1126/science.1232251. Epub 2012 Dec 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23239625" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Capping Proteins/chemistry/ultrastructure ; Actin Cytoskeleton/chemistry/ultrastructure ; Actins/chemistry/*ultrastructure ; Animals ; Axons/*chemistry/*ultrastructure ; Calmodulin-Binding Proteins/chemistry/*ultrastructure ; Cells, Cultured ; Cytoskeleton/*chemistry/*ultrastructure ; Dendrites/chemistry/ultrastructure ; Hippocampus/ultrastructure ; Image Processing, Computer-Assisted ; Microscopy, Fluorescence/methods ; Neurons/chemistry/ultrastructure ; Protein Multimerization ; Rats ; Rats, Wistar ; Sodium Channels/chemistry/ultrastructure ; Spectrin/chemistry/*ultrastructure
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Molecular biology. Unraveling DNA condensation with optical tweezers (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-07-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhuang, Xiaowei -- New York, N.Y. -- Science. 2004 Jul 9;305(5681):188-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA. zhuang@chemistry.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15247463" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Chromosomal Proteins, Non-Histone/chemistry/*metabolism ; DNA, Bacterial/*chemistry/*metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Dimerization ; Escherichia coli/genetics ; Escherichia coli Proteins/chemistry/*metabolism ; Lasers ; Microspheres ; Multiprotein Complexes ; *Nucleic Acid Conformation ; Protein Structure, Tertiary ; Protein Subunits ; Repressor Proteins/chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-11-15
    Description: The reverse transcriptase (RT) of human immunodeficiency virus (HIV) catalyzes a series of reactions to convert single-stranded viral RNA into double-stranded DNA for host cell integration. This process requires a variety of enzymatic activities, including DNA polymerization, RNA cleavage, strand transfer, and strand displacement synthesis. We used single-molecule fluorescence resonance energy transfer to probe the interactions between RT and nucleic acid substrates in real time. RT was observed to slide on nucleic acid duplexes, rapidly shuttling between opposite termini of the duplex. Upon reaching the DNA 3' terminus, RT can spontaneously flip into a polymerization orientation. Sliding kinetics were regulated by cognate nucleotides and anti-HIV drugs, which stabilized and destabilized the polymerization mode, respectively. These long-range translocation activities facilitate multiple stages of the reverse transcription pathway, including normal DNA polymerization and strand displacement synthesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717043/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717043/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Shixin -- Abbondanzieri, Elio A -- Rausch, Jason W -- Le Grice, Stuart F J -- Zhuang, Xiaowei -- GM 068518/GM/NIGMS NIH HHS/ -- R01 GM068518/GM/NIGMS NIH HHS/ -- R01 GM068518-05/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1092-7. doi: 10.1126/science.1163108.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008444" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbocyanines ; DNA Primers/metabolism ; DNA, Viral/biosynthesis/*metabolism ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes ; HIV Reverse Transcriptase/chemistry/*metabolism ; HIV-1/*enzymology ; Kinetics ; Models, Molecular ; Nevirapine/metabolism/pharmacology ; Nucleic Acid Hybridization ; Nucleotides/metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Viral/*metabolism ; Reverse Transcriptase Inhibitors/metabolism/pharmacology ; Reverse Transcription ; Ribonuclease H/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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