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Visualizing Biological Membrane Organization and Dynamics. J Mol Biol 2019; 431:1889-1919. [DOI: 10.1016/j.jmb.2019.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/02/2019] [Accepted: 02/13/2019] [Indexed: 11/22/2022]
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2
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Park SM, Yu H, Park MG, Han SY, Kang SW, Park HM, Kim JW. Quantitative analysis of an organic thin film by XPS, AFM and FT-IR. SURF INTERFACE ANAL 2011. [DOI: 10.1002/sia.3786] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Abstract
This overview unit provides a thorough overview of biophysical methods used for structure analysis, including X-ray diffraction, nuclear magnetic resonance, optical spectroscopy, theoretical and computational methods, and single-molecule methods. Advantages and disadvantages of the methods are compared.
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Affiliation(s)
- I Tinoco
- University of California, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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4
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Zheng Y, Wynne KJ. Poly(bis-2,2,2-trifluoroethoxymethyl oxetane): enhanced surface hydrophobicity by crystallization and spontaneous asperity formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:11964-11967. [PMID: 17958389 DOI: 10.1021/la702429p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report a spontaneous increase in the contact angle (104 degrees --> 136 degrees +/- 4 degrees ) for a semicrystalline polyoxetane with symmetrical CF3CH2OCH2 side chains. Poly(bis-trifluoroethoxymethyl)oxetane, P(B-3FOx), Mn = 21 kDa, was prepared by a modification of conventional cationic ring opening polymerization. At ambient temperature, the polymer is between Tg (-39 degrees C) and Tm (approximately 70 degrees C). Tapping mode atomic force microscopy (TM-AFM) revealed an interesting process-dependent topology. Coatings that were melted and slow-cooled displayed increasing roughness over the course of 4-6 weeks at 25 degrees C. The result was a topology characterized by sharp micrometer-scale ridges and asperities. The heat of fusion increases from an initial value of 21.9 J/g after slow cooling (non-isothermal melt crystallization) to 28 J/g after 6 weeks (non-isothermal melt crystallization plus isothermal melt crystallization). The coating appearance changes from transparent with a slight haze to translucent. The changing topology was accompanied by a 30 degrees increase in the water contact angle, up to 140 degrees , attributed to an asperity-rich surface yielding a discontinuous three-phase contact line and to a change in the proportions of crystalline and amorphous area fractions accompanying crystallization.
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Affiliation(s)
- Ying Zheng
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, 601 West Main Street, Richmond, VA 23284-3028, USA
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5
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Stolz M, Aebi U, Stoffler D. Developing scanning probe–based nanodevices—stepping out of the laboratory into the clinic. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2007; 3:53-62. [PMID: 17379169 DOI: 10.1016/j.nano.2007.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 07/19/2006] [Indexed: 10/23/2022]
Abstract
This report focuses on nanotools based on the scanning force microscope (SFM) for imaging, measuring, and manipulating biological matter at the sub-micron scale. Because pathophysiological processes often occur at the (sub-) cellular scale, the SFM has opened the exciting possibility to spot diseases at a stage before they become symptomatic and cause functional impairments in the affected part of the body. Such presymptomatic detection will be key to developing effective therapies to slow or halt disease progression.
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Affiliation(s)
- Martin Stolz
- M.E. Müller Institute for Structural Biology, Biozentrum, University of Basel, Switzerland
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6
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Toyabe SI, Akazawa K, Fukushi D, Fukui K, Ushiki T. CHRONIS: an animal chromosome image database. Chromosome Res 2005; 13:593-600. [PMID: 16170624 DOI: 10.1007/s10577-005-0985-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 05/27/2005] [Indexed: 11/29/2022]
Abstract
We have constructed a database system named CHRONIS (CHROmosome and Nano-Information System) to collect images of animal chromosomes and related nanotechnological information. CHRONIS enables rapid sharing of information on chromosome research among cell biologists and researchers in other fields via the Internet. CHRONIS is also intended to serve as a liaison tool for researchers who work in different centers. The image database contains more than 3,000 color microscopic images, including karyotypic images obtained from more than 1,000 species of animals. Researchers can browse the contents of the database using a usual World Wide Web interface in the following URL: http://chromosome.med.niigata-u.ac.jp/chronis/servlet/chronisservlet. The system enables users to input new images into the database, to locate images of interest by keyword searches, and to display the images with detailed information. CHRONIS has a wide range of applications, such as searching for appropriate probes for fluorescent in situ hybridization, comparing various kinds of microscopic images of a single species, and finding researchers working in the same field of interest.
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Affiliation(s)
- Shin-Ichi Toyabe
- Niigata University Medical and Dental Hospital, Niigata University, Asahi-machi-dori 1-754, Niigata 951-8520, Japan.
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7
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Vancso GJ, Hillborg H, Schönherr H. Chemical Composition of Polymer Surfaces Imaged by Atomic Force Microscopyand Complementary Approaches. POLYMER ANALYSIS POLYMER THEORY 2005. [DOI: 10.1007/b135560] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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8
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Hanton SD, Hyder IZ, Stets JR, Owens KG, Blair WR, Guttman CM, Giuseppetti AA. Investigations of electrospray sample deposition for polymer MALDI mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2004; 15:168-179. [PMID: 14766284 DOI: 10.1016/j.jasms.2003.09.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2003] [Revised: 09/15/2003] [Accepted: 09/28/2003] [Indexed: 05/24/2023]
Abstract
In the interest of a more thorough understanding of the relationship between sample deposition technique and the quality of data obtained using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, details of the electrospray (ES) process of sample deposition are investigated using a number of techniques. Sample morphology was observed with scanning electron microscopy (SEM) and atomic force microscopy (AFM), while matrix-enhanced secondary ion mass spectrometry (MESIMS) monitored surface coverage. Electrospray deposition reduces the analyte segregation that can occur during traditional dried droplet deposition for MALDI. We attribute statistically significant improvements in the reproducibility of signal intensity and MALDI average molecular mass measurements to the ES sample deposition technique.
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Affiliation(s)
- Scott D Hanton
- Air Products and Chemicals, Inc, Allentown, Pennsylvania 18195, USA.
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9
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Abstract
The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.
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Affiliation(s)
- H G Hansma
- Department of Physics, University of California, Santa Barbara, California 93106, USA.
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10
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Tegenfeldt JO, Bakajin O, Chou CF, Chan SS, Austin R, Fann W, Liou L, Chan E, Duke T, Cox EC. Near-field scanner for moving molecules. PHYSICAL REVIEW LETTERS 2001; 86:1378-1381. [PMID: 11178088 DOI: 10.1103/physrevlett.86.1378] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2000] [Indexed: 05/23/2023]
Abstract
We have fabricated using electron beam nanolithography a fixed slit near-field optical scanning device which uses near-field fluorimetry to achieve 200 nm spatial resolution of objects moving over the slits. We explore the basic physics of operating narrow slits in the waveguide cutoff mode and present data from the passage of extended double-stranded DNA molecules passing over the slits as a first example of how this device can be used to do ultrahigh spatial resolution mapping of long polymers.
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Affiliation(s)
- J O Tegenfeldt
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
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11
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Metzler DE, Metzler CM, Sauke DJ. Determining Structures and Analyzing Cells. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Li L, Chan CM, Yeung KL, Li JX, Ng KM, Lei Y. Direct Observation of Growth of Lamellae and Spherulites of a Semicrystalline Polymer by AFM. Macromolecules 2000. [DOI: 10.1021/ma000273e] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lin Li
- Department of Chemical Engineering, Advanced Engineering Materials Facility, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Chi-Ming Chan
- Department of Chemical Engineering, Advanced Engineering Materials Facility, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - King Lun Yeung
- Department of Chemical Engineering, Advanced Engineering Materials Facility, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Jian-Xiong Li
- Department of Chemical Engineering, Advanced Engineering Materials Facility, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Kai-Mo Ng
- Department of Chemical Engineering, Advanced Engineering Materials Facility, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Yuguo Lei
- Department of Chemical Engineering, Advanced Engineering Materials Facility, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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13
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Schönherr H, Hruska Z, Vancso GJ. Toward High Resolution Mapping of Functional Group Distributions at Surface-Treated Polymers by AFM Using Modified Tips. Macromolecules 2000. [DOI: 10.1021/ma991360d] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Holger Schönherr
- University of Twente, MESA+ Research Institute and Faculty of Chemical Technology, Materials Science and Technology of Polymers, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Alkor GmbH Kunststoffe, Morgensternstrasse 9, D-81479 München, Germany
| | - Zdenek Hruska
- University of Twente, MESA+ Research Institute and Faculty of Chemical Technology, Materials Science and Technology of Polymers, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Alkor GmbH Kunststoffe, Morgensternstrasse 9, D-81479 München, Germany
| | - G. Julius Vancso
- University of Twente, MESA+ Research Institute and Faculty of Chemical Technology, Materials Science and Technology of Polymers, P.O. Box 217, 7500 AE Enschede, The Netherlands, and Alkor GmbH Kunststoffe, Morgensternstrasse 9, D-81479 München, Germany
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Tamayo J, Miles M. Human chromosome structure studied by scanning force microscopy after an enzymatic digestion of the covering cell material. Ultramicroscopy 2000; 82:245-51. [PMID: 10741676 DOI: 10.1016/s0304-3991(99)00125-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In standard preparations, metaphase human chromosomes are covered by a cell material film composed mainly of proteins and RNA. This film (approximately 30 nm thickness) hides the chromosome structure to the tip of a scanning force microscope. In this work, a mild enzymatic treatment is applied to remove the cell material film. After treatment, the individual chromatin fibers at the surface were resolved. Furthermore, the chromosome shows a thickness modulation, in which thicker/thinner regions could be associated with G/R bands. Finally, the topography of the chromosomes in solution is presented. The chromosome volume swelled about five-fold and chromatin packaging in bands and coils was observed.
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Affiliation(s)
- J Tamayo
- H.H. Wills Physics Laboratory, University of Bristol, UK.
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15
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Tamayo J, Miles M, Thein A, Soothill P. Selective cleaning of the cell debris in human chromosome preparations studied by scanning force microscopy. J Struct Biol 1999; 128:200-10. [PMID: 10600573 DOI: 10.1006/jsbi.1999.4191] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The chromosome structure is one of most challenging biological structures to be discovered. Most evidence about the structure comes from optical microscopy. Scanning force microscopy (SFM) can achieve molecular resolution and allows imaging in liquids. However, little information about the chromosome structure has been revealed by SFM. In this work, a mild enzymatic treatment is applied to the chromosomes to remove selectively the RNA and proteins coming from the cell. The resulting SFM images indicate that a protein film with embedded RNA molecules covers chromosomes in standard cytogenetic preparations. The thickness of the protein layer is 15-35 nm and the RNA adheres preferentially to the chromosome surface. The cell material film results in a quite smooth chromosome surface without evidence of any structural detail. After treatment, the chromosome was cleaned from cell residues and individual chromatin fibers at the surface were resolved. Furthermore, insights about the higher order structure of the chromosome can be inferred.
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Affiliation(s)
- J Tamayo
- H. H. Wills Physics Laboratory, Fetal Medicine Research Unit, St. Michael's Hospital, University of Bristol, Tyndall Avenue, Bristol, BS8 1TL, United Kingdom.
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16
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Müller DJ, Baumeister W, Engel A. Controlled unzipping of a bacterial surface layer with atomic force microscopy. Proc Natl Acad Sci U S A 1999; 96:13170-4. [PMID: 10557292 PMCID: PMC23919 DOI: 10.1073/pnas.96.23.13170] [Citation(s) in RCA: 144] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/1999] [Accepted: 09/07/1999] [Indexed: 11/18/2022] Open
Abstract
We have combined high-resolution atomic force microscopy (AFM) imaging and force spectroscopy to gain insight into the interaction forces between the individual protomers of the hexagonally packed intermediate (HPI) layer of Deinococcus radiodurans. After imaging the HPI layer, the AFM stylus was attached to individual protomers by enforced stylus-sample contact to allow force spectroscopy experiments. Imaging of the HPI layer after recording force-extension curves allowed adhesion forces to be correlated with structural alterations. By using this approach, individual protomers of the HPI layer were found to be removed at pulling forces of approximately 300 pN. Furthermore, it was possible to sequentially unzip entire bacterial pores formed by six HPI protomers. The combination of high-resolution AFM imaging of individual proteins with the determination of their intramolecular forces is a method of studying the mechanical stability of supramolecular structures at the level of single molecules.
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Affiliation(s)
- D J Müller
- M. E. Müller-Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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Abstract
The highlight of the past year is the unfolding and refolding of the muscle protein titin in the atomic force microscope. A related highlight in the intersection between experiment and theory is a recent review of the effects of molecular forces on biochemical kinetics. Other advances in scanning probe microscopy include entropic brushes, molecular sandwiches and applications of atomic force microscopy to gene therapy.
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Affiliation(s)
- H G Hansma
- Department of Physics, University of California, Santa Barbara 93106, USA
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