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Beckwitt EC, Kong M, Van Houten B. Studying protein-DNA interactions using atomic force microscopy. Semin Cell Dev Biol 2017; 73:220-230. [PMID: 28673677 DOI: 10.1016/j.semcdb.2017.06.028] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022]
Abstract
Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.
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Affiliation(s)
- Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Muwen Kong
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA; The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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Single-molecule studies of high-mobility group B architectural DNA bending proteins. Biophys Rev 2016; 9:17-40. [PMID: 28303166 PMCID: PMC5331113 DOI: 10.1007/s12551-016-0236-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/19/2016] [Indexed: 11/23/2022] Open
Abstract
Protein–DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function. These roles vary from the maintenance of chromatin structure and facilitation of ribosomal RNA transcription (yeast high-mobility group 1 protein) to regulatory and packaging roles (human mitochondrial transcription factor A). We describe how these HMGB proteins bind, bend, bridge, loop and compact DNA to perform these functions. We also describe how single molecule experiments observe multiple rates for dissociation of HMGB proteins from DNA, while only one rate is observed in bulk experiments. The measured single-molecule kinetics reveals a local, microscopic mechanism by which HMGB proteins alter DNA flexibility, along with a second, much slower macroscopic rate that describes the complete dissociation of the protein from DNA.
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Liu T, Li Z, Lin Y, Song S, Zhang S, Sun L, Wang Y, Xu A, Bi Z, Wang X. Dynamic patterns of circulating influenza virus from 2005 to 2012 in Shandong Province, China. Arch Virol 2016; 161:3047-59. [PMID: 27515172 DOI: 10.1007/s00705-016-2997-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/26/2016] [Indexed: 11/25/2022]
Abstract
To identify circulating emerging/reemerging viral strains and epidemiological trends, an influenza sentinel surveillance network was established in Shandong Province, China, in 2005. Nasal and/or throat swabs from patients with influenza-like-illness were collected at sentinel hospitals. Influenza viruses were detected by reverse transcription polymerase chain reaction (RT-PCR) or virus isolation. From October 2005 to March 2012, 7763 (21.44 %) of 36,209 swab samples were positive for influenza viruses, including 5221 (67.25 %) influenza A and 2542 (32.75 %) influenza B. While the influenza viruses were detected year-round, their type/subtype distribution varied significantly. Peak influenza activity was observed from November to February. The proportion of laboratory-confirmed influenza cases was highest among participants aged 0-4 years (14.97 %) in the 2005-2009 and 2010-2012 influenza seasons and the positivity rate of influenza A(H1N1)pdm09 was highest in the 15 to 24 year age group during the 2009-2010 influenza season. Genetic analysis of hemagglutinin (HA) and neuraminidase (NA) genes revealed that the viruses matched seasonal influenza vaccine strains in general, with some amino acid mutations. Influenza A(H1N1)pdm09 strains isolated in Shandong Province were characterized by an S203T mutation that is specific to clade 7 isolates. This report illustrates that the Shandong Provincial influenza surveillance system was sensitive in detecting influenza virus variability by season and by genetic composition. This system will help official public health target interventions such as education programs and vaccines.
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Affiliation(s)
- Ti Liu
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Zhong Li
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Yi Lin
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Shaoxia Song
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Shengyang Zhang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Lin Sun
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Yulu Wang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Zhenqiang Bi
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China.
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China.
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Murugesapillai D, McCauley MJ, Huo R, Nelson Holte MH, Stepanyants A, Maher LJ, Israeloff NE, Williams MC. DNA bridging and looping by HMO1 provides a mechanism for stabilizing nucleosome-free chromatin. Nucleic Acids Res 2014; 42:8996-9004. [PMID: 25063301 PMCID: PMC4132745 DOI: 10.1093/nar/gku635] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The regulation of chromatin structure in eukaryotic cells involves abundant architectural factors such as high mobility group B (HMGB) proteins. It is not understood how these factors control the interplay between genome accessibility and compaction. In vivo, HMO1 binds the promoter and coding regions of most ribosomal RNA genes, facilitating transcription and possibly stabilizing chromatin in the absence of histones. To understand how HMO1 performs these functions, we combine single molecule stretching and atomic force microscopy (AFM). By stretching HMO1-bound DNA, we demonstrate a hierarchical organization of interactions, in which HMO1 initially compacts DNA on a timescale of seconds, followed by bridge formation and stabilization of DNA loops on a timescale of minutes. AFM experiments demonstrate DNA bridging between strands as well as looping by HMO1. Our results support a model in which HMO1 maintains the stability of nucleosome-free chromatin regions by forming complex and dynamic DNA structures mediated by protein–protein interactions.
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Affiliation(s)
| | - Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Ran Huo
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - Molly H Nelson Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Armen Stepanyants
- Department of Physics, Northeastern University, Boston, MA 02115, USA
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | | | - Mark C Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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Coats JE, Lin Y, Rueter E, Maher LJ, Rasnik I. Single-molecule FRET analysis of DNA binding and bending by yeast HMGB protein Nhp6A. Nucleic Acids Res 2013; 41:1372-81. [PMID: 23221634 PMCID: PMC3554232 DOI: 10.1093/nar/gks1208] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/02/2012] [Accepted: 10/30/2012] [Indexed: 02/06/2023] Open
Abstract
High-mobility group B (HMGB) proteins bind duplex DNA without sequence specificity, facilitating the formation of compact nucleoprotein structures by increasing the apparent flexibility of DNA through the introduction of DNA kinks. It has remained unclear whether HMGB binding and DNA kinking are simultaneous and whether the induced kink is rigid (static) or flexible. The detailed molecular mechanism of HMGB-induced DNA 'softening' is explored here by single-molecule fluorescence resonance energy transfer studies of single yeast Nhp6A (yNhp6A) proteins binding to short DNA duplexes. We show that the local effect of yNhp6A protein binding to DNA is consistent with formation of a single static kink that is short lived (lifetimes of a few seconds) under physiological buffer conditions. Within the time resolution of our experiments, this static kink occurs at the instant the protein binds to the DNA, and the DNA straightens at the instant the protein dissociates from the DNA. Our observations support a model in which HMGB proteins soften DNA through random dynamic binding and dissociation, accompanied by DNA kinking and straightening, respectively.
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Affiliation(s)
- Julie E. Coats
- Department of Physics, Emory University, 30322 Atlanta, GA
and Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester,
38105 MN, USA
| | - Yuyen Lin
- Department of Physics, Emory University, 30322 Atlanta, GA
and Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester,
38105 MN, USA
| | - Emily Rueter
- Department of Physics, Emory University, 30322 Atlanta, GA
and Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester,
38105 MN, USA
| | - L. James Maher
- Department of Physics, Emory University, 30322 Atlanta, GA
and Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester,
38105 MN, USA
| | - Ivan Rasnik
- Department of Physics, Emory University, 30322 Atlanta, GA
and Department of Biochemistry & Molecular Biology, Mayo Clinic, Rochester,
38105 MN, USA
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McCauley MJ, Rueter EM, Rouzina I, Maher LJ, Williams MC. Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility. Nucleic Acids Res 2012; 41:167-81. [PMID: 23143110 PMCID: PMC3592474 DOI: 10.1093/nar/gks1031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacing neutral N-terminal residues of the HMGB2 protein with cationic sequences from Nhp6Ap. Surprisingly, HMGB proteins constrain DNA winding, and this torsional constraint is released over short timescales. These measurements reveal the microscopic dissociation rates of HMGB from DNA. Separate microscopic and macroscopic (or local and non-local) unbinding rates have been previously proposed, but never independently observed. Microscopic dissociation rates for the chimeric mutants (∼10 s−1) are higher than those observed for wild-type proteins (∼0.1–1.0 s−1), reflecting their reduced ability to bend DNA through short-range interactions, despite their increased DNA-binding affinity. Therefore, transient local HMGB–DNA contacts dominate the DNA-bending mechanism used by these important architectural proteins to increase DNA flexibility.
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Affiliation(s)
- Micah J McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA
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