STM and AFM of bio/organic molecules and structures

Abstract Applications of scanning tunneling and atomic force microscopes in bio/organic researches are reviewed with a special emphasis on the types of researches that are expected to contribute to the creation of a new field of “single molecule biochemistry” in the near future. The reviewed articles within the scope as stated above actually include a fairly broad spectrum of researches. It is, therefore, a hope of the author that this review will be useful to those who are considering biological applications of the probe microscopy techniques but are not quite familiar with the types of experiments that have been done in the past. In the section on scanning tunneling microscopy, identification of chemically distinct functional groups by the difference in their tunneling properties will be discussed as a main focus because it is fundamental for biochemists to identify molecules by their shapes and properties. In the section on atomic force microscopy, recent progresses in the imaging techniques of proteins and DNAs are closely reviewed, and rapidly advancing technologies of single molecule measurements and manipulation of nanometer sized structures are given extensive coverage because the author considers that such new applications are extremely promising to open an entirely new field in biological sciences.

[1]  G. Rummel,et al.  Crystal structures explain functional properties of two E. coli porins , 1992, Nature.

[2]  H. Butt,et al.  Measuring electrostatic, van der Waals, and hydration forces in electrolyte solutions with an atomic force microscope. , 1991, Biophysical journal.

[3]  A Engel,et al.  Biological applications of scanning probe microscopes. , 1991, Annual review of biophysics and biophysical chemistry.

[4]  M. Hegner,et al.  Immobilizing DNA on gold via thiol modification for atomic force microscopy imaging in buffer solutions , 1993, FEBS letters.

[5]  J. Bechhoefer,et al.  Calibration of atomic‐force microscope tips , 1993 .

[6]  J. Frommer,et al.  Friction measurements on phase-separated thin films with a modified atomic force microscope , 1992, Nature.

[7]  P. Descouts,et al.  Atomic force microscopy under liquid: A comparative study of three different AC mode operations , 1995 .

[8]  P K Hansma,et al.  Direct observation of enzyme activity with the atomic force microscope. , 1994, Science.

[9]  A. Stemmer A hybrid scanning force and light microscope for surface imaging and three‐dimensional optical sectioning in differential interference contrast , 1995, Journal of microscopy.

[10]  R. Emch,et al.  Scanning force microscopy and cryo-electron microscopy of tobacco mosaic virus as a test specimen. , 1992, Ultramicroscopy.

[11]  Z. Shao,et al.  Molecular resolution atomic force microscopy of soluble proteins in solution. , 1994, Biochimica et biophysica acta.

[12]  P. J. Bryant,et al.  Atomic force microscopy of purple membranes , 1988, Journal of microscopy.

[13]  C. J. Chen,et al.  Introduction to Scanning Tunneling Microscopy , 1993 .

[14]  D. Anselmetti,et al.  Binding strength between cell adhesion proteoglycans measured by atomic force microscopy , 1995, Science.

[15]  S Lees,et al.  Measuring the microelastic properties of biological material. , 1992, Biophysical journal.

[16]  T. Kawai,et al.  Distinct imaging of the nucleic acid bases on SrTiO3(100) surface by scanning tunneling microscopy , 1995 .

[17]  A. Engel,et al.  Native Escherichia coli OmpF porin surfaces probed by atomic force microscopy. , 1995, Science.

[18]  F. Giessibl,et al.  Atomic Resolution of the Silicon (111)-(7x7) Surface by Atomic Force Microscopy , 1995, Science.

[19]  H. Butt,et al.  Quantitative scanning tunneling microscopy and scanning force microscopy of organic materials , 1992 .

[20]  M. Hegner,et al.  Covalent immobilization of native biomolecules onto Au(111) via N-hydroxysuccinimide ester functionalized self-assembled monolayers for scanning probe microscopy. , 1996, Biophysical journal.

[21]  Analysis of immunolabeled cells by atomic force microscopy, optical microscopy, and flow cytometry. , 1994, Journal of structural biology.

[22]  T M Jovin,et al.  Imaging subcellular structures of rat mammary carcinoma cells by scanning force microscopy. , 1994, Journal of cell science.

[23]  K. Takayanagi,et al.  Structural analysis of Si(111)‐7×7 by UHV‐transmission electron diffraction and microscopy , 1985 .

[24]  J. Zasadzinski,et al.  Coexisting Lattice Structures in a Langmuir-Blodgett Film Identified by Atomic Force Microscopy , 1993 .

[25]  Paul K. Hansma,et al.  Tapping mode atomic force microscopy in liquids , 1994 .

[26]  Z. Shao,et al.  Atomic force microscopy of DNA molecules , 1992, FEBS letters.

[27]  H. Nejoh Visible mechanism of liquid crystals on graphite under scanning tunneling microscopy , 1990 .

[28]  E. Stoll,et al.  Scanning tunneling microscopy of individual molecules of copper phthalocyanine adsorbed on polycrystalline silver surfaces , 1987 .

[29]  N. Clark,et al.  Near—Atomic Resolution Imaging of Ferroelectric Liquid Crystal Molecules on Graphite by STM , 1995, Science.

[30]  J. Garnaes,et al.  Surface Order and Stability of Langmuir-Blodgett Films , 1992, Science.

[31]  R. Wilson,et al.  Scanning Tunneling Microscopy Observations of Benzene Molecules on the Rh(111)-(3×3) (C6H6+2CO) Surface , 1988 .

[32]  O. Marti,et al.  STM and SFM in Biology , 1994 .

[33]  A. Ikai,et al.  Method for immobilizing microbial cells on gel surface for dynamic AFM studies. , 1995, Biophysical journal.

[34]  G E Sosinsky,et al.  Structure of the extracellular surface of the gap junction by atomic force microscopy. , 1993, Biophysical journal.

[35]  J. Frommer,et al.  Molecular-resolution images of Langmuir–Blodgett films using atomic force microscopy , 1991, Nature.

[36]  P. Hough,et al.  Recent advances in atomic force microscopy of DNA. , 1993, Scanning.

[37]  C. Siegerist,et al.  Reproducible Imaging and Dissection of Plasmid DNA Under Liquid with the Atomic Force Microscope , 1992, Science.

[38]  Gil U. Lee,et al.  Direct measurement of the forces between complementary strands of DNA. , 1994, Science.

[39]  J. Zasadzinski,et al.  Strained-layer van der Waals epitaxy in a Langmuir-Blodgett film. , 1993, Science.

[40]  Direct visualization of polypeptide shell of ferritin molecule by atomic force microscopy. , 1993, Biophysical journal.

[41]  Sakurai,et al.  Intramolecular structures of C60 molecules adsorbed on the Cu(111)-(1 x 1) surface. , 1993, Physical review letters.

[42]  R. Henderson,et al.  Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. , 1990, Journal of molecular biology.

[43]  L. Bourdieu,et al.  Molecular Positional Order in Langmuir-Blodgett Films by Atomic Force Microscopy , 1993, Science.

[44]  H. White,et al.  Scanning Tunneling Microscopy, Atomic Force Microscopy, and Related Techniques. , 1992 .

[45]  K. Matsushige,et al.  Direct observation of the growth process of organic crystals by scanning tunnelling microscopy , 1993 .

[46]  M. Radmacher,et al.  Imaging viscoelasticity by force modulation with the atomic force microscope. , 1993, Biophysical journal.

[47]  G. Binnig,et al.  True Atomic Resolution by Atomic Force Microscopy Through Repulsive and Attractive Forces , 1993, Science.

[48]  J. Vesenka,et al.  A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy. , 1995, Nucleic acids research.

[49]  William J. Kaiser,et al.  Scanning Tunneling Microscopy , 2019, CIRP Encyclopedia of Production Engineering.

[50]  Paul K. Hansma,et al.  Molecular-resolution images of Langmuir-Blodgett films and DNA by atomic force microscopy , 1991 .

[51]  H. Lang,et al.  Imaging C60 fullerite at 4.5 K by scanning tunneling microscopy , 1993 .

[52]  J. Zasadzinski,et al.  The structure and stability of phospholipid bilayers by atomic force microscopy. , 1995, Biophysical journal.

[53]  F. Sommer,et al.  Atomic force microscopy study of the collagen fibre structure , 1994, Biology of the cell.

[54]  T. Jovin,et al.  Probing specific molecular conformations with the scanning force microscope. Complexes of plasmid DNA and anti-Z-DNA antibodies. , 1994, Nucleic Acids Research.

[55]  H. Butt,et al.  Electrostatic interaction in atomic force microscopy. , 1991, Biophysical journal.

[56]  A. Stemmer,et al.  Miniature-size scanning tunneling microscope with integrated 2-axes heterodyne interferometer and light microscope , 1988 .

[57]  P K Hansma,et al.  Imaging the membrane protein bacteriorhodopsin with the atomic force microscope. , 1990, Biophysical journal.

[58]  Y. Lyubchenko,et al.  Atomic force microscopy of reovirus dsRNA: a routine technique for length measurements. , 1992, Nucleic acids research.

[59]  H. Hansma,et al.  Applications for atomic force microscopy of DNA. , 1995, Biophysical journal.

[60]  R. Lal,et al.  Atomic force microscopy and dissection of gap junctions , 1991, Science.

[61]  P. Bennema,et al.  Scanning tunneling microscopy studies on n‐alkane molecules adsorbed on graphite , 1994 .

[62]  E. Henderson,et al.  Imaging and nanodissection of individual supercoiled plasmids by atomic force microscopy. , 1992, Nucleic acids research.

[63]  D. Chatenay,et al.  Imaging surface of gold‐immunolabeled thin sections by atomic force microscopy , 1994 .

[64]  M. Morra,et al.  Atomic force microscopy studies of the interaction of a dentin adhesive with tooth hard tissue. , 1994, Journal of Biomedical Materials Research.

[65]  H. Sasabe,et al.  Anchoring structure of smectic liquid-crystal layers on MoS2 observed by scanning tunnelling microscopy , 1990, Nature.

[66]  M. Ohta,et al.  Defect Motion on an InP(110) Surface Observed with Noncontact Atomic Force Microscopy , 1995, Science.

[67]  Ryo Kuroda,et al.  Barrier-height imaging of fatty acid Langmuir-Blodgett films , 1992 .

[68]  H. Gaub,et al.  Adhesion forces between individual ligand-receptor pairs. , 1994, Science.

[69]  C. Bustamante,et al.  Circular DNA molecules imaged in air by scanning force microscopy. , 1992, Biochemistry.

[70]  H. Hansma,et al.  Bending and straightening of DNA induced by the same ligand: characterization with the atomic force microscope. , 1994, Biochemistry.

[71]  T. Beebe,et al.  Graphite: a mimic for DNA and other biomolecules in scanning tunneling microscope studies. , 1991, Science.

[72]  R. E. Weber,et al.  Work function and structural studies of alkali-covered semiconductors , 1969 .

[73]  I. N. Sneddon The relation between load and penetration in the axisymmetric boussinesq problem for a punch of arbitrary profile , 1965 .

[74]  Udo D. Schwarz,et al.  Tip artefacts in scanning force microscopy , 1994 .

[75]  A. Bonfiglio,et al.  Subcellular details of early events of differentiation induced by retinoic acid in human neuroblastoma cells detected by atomic force microscope. , 1995, Experimental cell research.

[76]  S. Tang,et al.  New internal structure of spider dragline silk revealed by atomic force microscopy. , 1994, Biophysical journal.

[77]  B. Venkataraman,et al.  Scanning Tunneling Microscopy Studies of Solvent Effects on the Adsorption and Mobility of Triacontane/Triacontanol Molecules Adsorbed on Graphite , 1995 .

[78]  Wen-Ling Shaiu,et al.  Atomic force microscopy of oriented linear DNA molecules labeled with 5nm gold spheres , 1993, Nucleic Acids Res..

[79]  T. Jovin,et al.  The scanning force microscopy of DNA in air and in n‐propanol using new spreading agents , 1994, FEBS letters.

[80]  M. Radmacher,et al.  Granula motion and membrane spreading during activation of human platelets imaged by atomic force microscopy. , 1994, Biophysical journal.

[81]  A Ikai,et al.  A method for anchoring round shaped cells for atomic force microscope imaging. , 1995, Biophysical journal.

[82]  Tomoji Kawai,et al.  Scanning tunneling microscopy observation and theoretical calculation of the adsorption of adenine on Si(100)2 × 1 surfaces , 1995 .

[83]  P. J. Bryant,et al.  Imaging bacteriorhodopsin lattices in purple membranes with atomic force microscopy , 1990 .

[84]  E. Bamberg,et al.  Scan speed limit in atomic force microscopy , 1993 .

[85]  W. Baumeister,et al.  A scanning tunneling microscope (STM) for biological applications: design and performance. , 1988, Ultramicroscopy.

[86]  T. Thundat,et al.  STM and AFM images of nucleosome DNA under water. , 1989, Journal of biomolecular structure & dynamics.

[87]  S. Buchholz,et al.  Commensurability and Mobility in Two-Dimensional Molecular Patterns on Graphite , 1991, Science.

[88]  H. Hansma,et al.  Atomic force microscopy of DNA in aqueous solutions. , 1993, Nucleic acids research.

[89]  A. C. Hillier,et al.  Atomic Force Microscopy of the Electrochemical Nucleation and Growth of Molecular Crystals , 1994, Science.

[90]  M. Hegner,et al.  Specific antigen/antibody interactions measured by force microscopy. , 1996, Biophysical journal.

[91]  Tip-Sample Interactions in Atomic Force Microscopy: I. Modulating Adhesion Between Silicon Nitride and Glass , 1991 .

[92]  Atomic force microscopy of three-dimensional membrane protein crystals. Ca-ATPase of sarcoplasmic reticulum. , 1992, Biophysical journal.

[93]  S. Tang,et al.  Internal structure of Kevlar® fibres by atomic force microscopy , 1993 .

[94]  Scanning Tunneling and Atomic Force Microscopy of T4 Bacteriophage and Tobacco Mosaic Virus , 1993 .

[95]  Paul K. Hansma,et al.  Imaging adhesion forces and elasticity of lysozyme adsorbed on mica with the atomic force microscope , 1994 .

[96]  H. Hansma,et al.  DNA binding to mica correlates with cationic radius: assay by atomic force microscopy. , 1996, Biophysical journal.

[97]  D. F. Ogletree,et al.  Atomic force microscopy imaging of T4 bacteriophages on silicon substrates. , 1991, Ultramicroscopy.

[98]  A. Ikai,et al.  Atomic force microscope of bacteriophage T4 and its tube‐baseplate complex , 1993, FEBS letters.

[99]  H. Hansma,et al.  Motion and enzymatic degradation of DNA in the atomic force microscope. , 1994, Biophysical journal.

[100]  P K Hansma,et al.  Atomic force microscopy for high-resolution imaging in cell biology. , 1992, Trends in cell biology.

[101]  E. Gilson,et al.  Imaging the asymmetrical DNA bend induced by repressor activator protein 1 with scanning tunneling microscopy. , 1994, Journal of structural biology.

[102]  N. Rampino Cisplatin induced alterations in oriented fibers of DNA studied by atomic force microscopy. , 1992, Biochemical and biophysical research communications.

[103]  J. Israelachvili Intermolecular and surface forces , 1985 .

[104]  C. Ascoli,et al.  An atomic force microscope for cytological and histological investigations , 1994, Journal of microscopy.

[105]  H. Sasabe,et al.  Imaging the ordered arrays of water-soluble protein ferritin with the atomic force microscope. , 1992, Biophysical journal.

[106]  H. Butt,et al.  Measuring local surface charge densities in electrolyte solutions with a scanning force microscope. , 1992, Biophysical journal.

[107]  J. Frommer,et al.  PROGRESS IN NONCONTRACT DYNAMIC FORCE MICROSCOPY , 1994 .

[108]  Wilson,et al.  High-resolution imaging of copper-phthalocyanine by scanning-tunneling microscopy. , 1989, Physical review letters.

[109]  M Heim,et al.  Scanning tunneling microscopy of insulators and biological specimens based on lateral conductivity of ultrathin water films. , 1994, Science.

[110]  T. Thundat,et al.  Imaging isolated strands of DNA molecules by atomic force microscopy. , 1992, Ultramicroscopy.

[111]  C F Quate,et al.  Imaging crystals, polymers, and processes in water with the atomic force microscope. , 1989, Science.

[112]  P. Hansma,et al.  Imaging purple membranes dry and in water with the atomic force microscope , 1991 .

[113]  H. Sasabe,et al.  Correlation Between Bulk Orderings and Anchoring Structures of Liquid Crystals Studied by Scanning Tunneling Microscopy , 1991 .

[114]  D. Braunstein,et al.  Structure and activation dynamics of RBL-2H3 cells observed with scanning force microscopy. , 1994, Biophysical journal.

[115]  Z. Shao,et al.  Atomic force microscopy of cholera toxin B-oligomers bound to bilayers of biologically relevant lipids. , 1995, Journal of molecular biology.

[116]  H. Butt Electrostatic interaction in scanning probe microscopy when imaging in electrolyte solutions , 1992 .

[117]  H. Hansma,et al.  Atomic force microscopy of single- and double-stranded DNA. , 1992, Nucleic acids research.

[118]  N. Batina,et al.  Self-Organized Porphyrin Array on Iodine-Modified Au(111) in Electrolyte Solutions: In Situ Scanning Tunneling Microscopy Study , 1995 .

[119]  C. le Grimellec,et al.  Imaging of the membrane surface of MDCK cells by atomic force microscopy. , 1994, Biophysical journal.

[120]  M. Radmacher,et al.  Protein tracking and detection of protein motion using atomic force microscopy. , 1996, Biophysical journal.

[121]  E. Meyer,et al.  Forces in scanning probe methods , 1995 .

[122]  P. Descouts,et al.  Influence of surface and protein modification on immunoglobulin G adsorption observed by scanning force microscopy. , 1994, Biophysical journal.

[123]  G Büldt,et al.  Imaging purple membranes in aqueous solutions at sub-nanometer resolution by atomic force microscopy. , 1995, Biophysical journal.

[124]  M. Hibino,et al.  Atomic Images of Saturated and Unsaturated Fatty Acids at Liquid/Graphite Interface and Difference of Tunneling Currents between Them Observed by Scanning Tunneling Microscopy , 1995 .

[125]  Y. Lyubchenko,et al.  Atomic force microscopy of DNA and bacteriophage in air, water and propanol: the role of adhesion forces. , 1993, Nucleic acids research.

[126]  M. Arnsdorf,et al.  Calibration of the scanning (atomic) force microscope with gold particles , 1994, Journal of microscopy.

[127]  C. Bustamante,et al.  Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. , 1993, Science.

[128]  A. Ikai,et al.  Mechanical unfolding of a2‐macroglobulin molecules with atomic force microscope , 1996 .

[129]  M. Boogaerts,et al.  Imaging uremic red blood cells with the atomic force microscope. , 1994, American journal of nephrology.

[130]  N. Rodríguez-Hornedo,et al.  The influence of additives on the growth kinetics and mechanism of l-alanine crystals , 1995 .

[131]  D. Ivey,et al.  Preparation of sharp polycrystalline tungsten tips for scanning tunneling microscopy imaging , 1996 .

[132]  Butt,et al.  Measuring adhesion, attraction, and repulsion between surfaces in liquids with an atomic-force microscope. , 1992, Physical review. B, Condensed matter.

[133]  P. Hansma,et al.  Scanning Tunneling Microscopy and Atomic Force Microscopy of Biological Surfaces a , 1990 .

[134]  S. Timoshenko,et al.  Theory of elasticity , 1975 .

[135]  P. Hansma,et al.  A nondestructive method for determining the spring constant of cantilevers for scanning force microscopy , 1993 .

[136]  Henny W. Zandbergen,et al.  Evaluation of the probing profile of scanning force microscopy tips , 1994 .

[137]  P. Hansma,et al.  Lattice resolution and solution kinetics on surfaces of amino acid crystals: an atomic force microscope study , 1993 .

[138]  J. Vesenka,et al.  Atomic force microscopy of uncoated plasmid DNA: nanometer resolution with only nanogram amounts of sample. , 1992, Journal of biomolecular structure & dynamics.

[139]  M. Radmacher,et al.  Imaging soft samples with the atomic force microscope: gelatin in water and propanol. , 1995, Biophysical journal.

[140]  M. Radmacher,et al.  Mapping interaction forces with the atomic force microscope. , 1994, Biophysical Journal.

[141]  H. Butt,et al.  Imaging flagella of halobacteria by atomic force microscopy , 1994 .

[142]  S. Quake,et al.  Relaxation of a single DNA molecule observed by optical microscopy. , 1994, Science.

[143]  Paul K. Hansma,et al.  Quantized adhesion detected with the atomic force microscope , 1992 .

[144]  H. Hansma,et al.  Biomolecular imaging with the atomic force microscope. , 1994, Annual review of biophysics and biomolecular structure.

[145]  J. Baldeschwieler,et al.  Atomic-scale imaging of DNA using scanning tunnelling microscopy , 1990, Nature.