406 Index Protein unfolding, AFM studies (continued ) single-parameter model, 325–327 sorting data, 321 Protomers, bacterial pore unzipping, 287 Q QPD, see Quadrant photodiode Quadrant photodiode, PFM studies, 203–204 R Recording mode photonic force microscopy contact mode, 208–209 fast 3D single-particle tracking, 210 tapping mode, 209–210 Resolution, PFM studies, 207–208 RL cells, adhesion force measurements, 100–104 S Salt, SFM of supercoiled DNA, 385–388 SATP, see N-Succinnimidyl-3-(S-acetylthio)propionate Scanning force microscopy DNA AC modes, 367 covalent, anchoring, 365–366 electron microscope legacy, 359 fragment ablation, 379 mobility modulation and solution dynamics, 371–374 molecular motion, 374–376 organic solvents, humidity issue, 366–367 protein interactions, 376–377 protein and ligand interactions, 368–369 secondary structure, 369–370 sharper probes, 367–368 single-molecule dissection, 377–379 single-molecule stretching, 388 solid-state sizing, 370 ss-DNA structure, 388 supercoiled, salt and surface effects, 385–388 water and buffers, 370–371 DNA curvature and flexibility basic approaches, 380–384 ergodicity, 384–385 scanning forces, 54–56 Scanning nearfield optical microscopy, 4 Scanning tunneling microscopy bacteriophage T5, 4–7 instrumentation and function, 2 liquid crystals, 6 Sensory cells, live, AFM studies, 38 SFM, see Scanning force microscopy SGLT1, see Na + /D-glucose cotransporter Silane, treatment of DNA on mica, 360–361 Single-molecule force, 292 Single-particle tracking, fast 3D, PFM studies, 210 Single-stranded DNA, SFM studies, 388 Small unilamellar vesicles, fusion, AFM studies, 232–234 SNOM, see Scanning nearfield optical microscopy Soft samples, AFM force curves, 70 Solid-state sizing, SFM of DNA, 370 Solutions, DNA adsorption, charged molecule role, 364 mica, dehydration, 360 SFM studies, 371–374 Spectrin, AFM studies, 313 Staphylococcal α-hemolysin, AFM studies, 270 Stereocilia, 144–146 STM, see Scanning tunneling microscopy Strain, induced, AFM calculations, 181–182 Streptavidin–biotin unbinding, AFM studies, 306–307 Structural biology, cryo-AFM individual molecules, 248–250 large assembly surface details, 250–252 Substrates, AFM studies, 215 N-Succinnimidyl-3-(S-acetylthio)propionate, AFM tips, 119 Supported lipid bilayers, AFM studies Langmuir trough, 234–235 Langmuir trough and small Teflon wells, 235–236 small vesicle fusion, 232–234 Surface chemistry, AFM studies basic studies, 215 cleaning, 117–118 crosslinker binding, 119 esterification, 118 large assemblies, cryo-AFM studies, 250–252 ligand binding, 119 ligand density and functionality, 119–120 probe surfaces, 120–121 Surfaces SFM of supercoiled DNA, 385–388 treatments for DNA adsorption, 365 SUVs, see Small unilamellar vesicles T Tapping mode atomic force microscopy basic operation, 35 Index 407 benefits, 338–339 overview, 261–263 Tapping recording mode photonic force microscopy, 209–210 TDFM, see Transverse dynamic force microscopy Teflon, small wells, AFM studies, 235–236 TEM, see Transmission electron microscopy Thermodynamics equilibrium, DNA on mica, 363–364 vascular endothelial cadherin, 129–130 Transduction channel, OHC, gating, 161–165 Transient fusion, depressions, AFM studies, 43–47 trans-interaction force, vascular endothelial cadherin, 127–128 Transmission electron microscopy bacteriophage T5, STM comparison, 6–7 transient fusions at depressions, 46 Transverse dynamic force microscopy application, 353–354 overview, 352–353 Transverse dynamic force spectroscopy application, 353–354 overview, 351–353 U Unbinding force, ligand–receptor recognition distribution, 123 dynamic force microscopy, 124–125 force–distance cycle, 121–123 V Vascular endothelial cells, cadherin, dynamic force microscopy binding strength, 128–129 Ca 2+ dependence, 127–128 conformation, 126 overview, 125–126 thermodynamics and structural parameters, 129–130 trans association, 127–128 VE cells, see Vascular endothelial cells VIP receptor, mapping on osteoclasts, 184 Viscosity, local, PFM studies, 28–29 Voltage-sensitive ion channels, AFM–path–clamp combination, 12–13 W Water, SFM of DNA, 370–371 WLC, see Worm-like chain model Worm-like chain model, protein folding, 17 Y Yeast cells, AFM studies, 38 Z z-range scanner, AFM, 177 Zymogen granules, AFM studies, 39 This Page Intentionally Left Blank VOLUMES IN SERIES Founding Series Editor DAVID M. PRESCOTT Volume 1 (1964) Methods in Cell Physiology Edited by David M. Prescott Volume 2 (1966) Methods in Cell Physiology Edited by David M. Prescott Volume 3 (1968) Methods in Cell Physiology Edited by David M. Prescott Volume 4 (1970) Methods in Cell Physiology Edited by David M. Prescott Volume 5 (1972) Methods in Cell Physiology Edited by David M. Prescott Volume 6 (1973) Methods in Cell Physiology Edited by David M. Prescott Volume 7 (1973) Methods in Cell Biology Edited by David M. Prescott Volume 8 (1974) Methods in Cell Biology Edited by David M. Prescott Volume 9 (1975) Methods in Cell Biology Edited by David M. Prescott 409 410 Volumes in Series Volume 10 (1975) Methods in Cell Biology Edited by David M. Prescott Volume 11 (1975) Yeast Cells Edited by David M. Prescott Volume 12 (1975) Yeast Cells Edited by David M. Prescott Volume 13 (1976) Methods in Cell Biology Edited by David M. Prescott Volume 14 (1976) Methods in Cell Biology Edited by David M. Prescott Volume 15 (1977) Methods in Cell Biology Edited by David M. Prescott Volume 16 (1977) Chromatin and Chromosomal Protein Research I Edited by Gary Stein, Janet Stein, and Lewis J. Kleinsmith Volume 17 (1978) Chromatin and Chromosomal Protein Research II Edited by Gary Stein, Janet Stein, and Lewis J. Kleinsmith Volume 18 (1978) Chromatin and Chromosomal Protein Research III Edited by Gary Stein, Janet Stein, and Lewis J. Kleinsmith Volume 19 (1978) Chromatin and Chromosomal Protein Research IV Edited by Gary Stein, Janet Stein, and Lewis J. Kleinsmith Volume 20 (1978) Methods in Cell Biology Edited by David M. Prescott Volumes in Series 411 Advisory Board Chairman KEITH R. PORTER Volume 21A (1980) Normal Human Tissue and Cell Culture, Part A: Respiratory, Cardiovascular, and Integumentary Systems Edited by Curtis C. Harris, Benjamin F. Trump, and Gary D. 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Goldstein and Eric A. Fyrberg Volume 45 (1994) Microbes as Tools for Cell Biology Edited by David G. Russell Volume 46 (1995) (in preparation) Cell Death Edited by Lawrence M. Schwartz and Barbara A. Osborne Volume 47 (1995) Cilia and Flagella Edited by William Dentler and George Witman Volume 48 (1995) Caenorhabditis elegans: Modern Biological Analysis of an Organism Edited by Henry F. Epstein and Diane C. Shakes Volume 49 (1995) Methods in Plant Cell Biology, Part A Edited by David W. Galbraith, Hans J. Bohnert, and Don P. Bourque 414 Volumes in Series Volume 50 (1995) Methods in Plant Cell Biology, Part B Edited by David W. Galbraith, Don P. Bourque, and Hans J. Bohnert Volume 51 (1996) Methods in Avian Embryology Edited by Marianne Bronner-Fraser Volume 52 (1997) Methods in Muscle Biology Edited by Charles P. Emerson, Jr. and H. Lee Sweeney Volume 53 (1997) Nuclear Structure and Function Edited by Miguel Berrios Volume 54 (1997) Cumulative Index Volume 55 (1997) Laser Tweezers in Cell Biology Edited by Michael P. Sheez Volume 56 (1998) Video Microscopy Edited by Greenfield Sluder and David E. Wolf Volume 57 (1998) Animal Cell Culture Methods Edited by Jennie P. Mather and David Barnes Volume 58 (1998) Green Fluorescent Protein Edited by Kevin F. Sullivan and Steve A. Kay Volume 59 (1998) The Zebrafish: Biology Edited by H. William Detrich III, Monte Westerfield, and Leonard I. Zon Volume 60 (1998) The Zebrafish: Genetics and Genomics Edited by H. William Detrich III, Monte Westerfield, and Leonard I. Zon Volume 61 (1998) Mitosis and Meiosis Edited by Conly L. Rieder Volumes in Series 415 Volume 62 (1999) Tetrahymena thermophila Edited by David J. Asai and James D. Forney Volume 63 (2000) Cytometry, Third Edition, Part A Edited by Zbigniew Darzynkiewicz, J. Paul Robinson, and Harry Crissman Volume 64 (2000) Cytometry, Third Edition, Part B Edited by Zbigniew Darzynkiewicz, J. Paul Robinson, and Harry Crissman Volume 65 (2001) Mitochondria Edited by Liza A. Pon and Eric A. Schon Volume 66 (2001) Apoptosis Edited by Lawrence M. Schwartz and Jonathan D. Ashwell . recognition distribution, 123 dynamic force microscopy, 124 – 125 force distance cycle, 121 – 123 V Vascular endothelial cells, cadherin, dynamic force microscopy binding strength, 128 – 129 Ca 2+ dependence, 127 – 128 conformation,. studies, 20 3 20 4 R Recording mode photonic force microscopy contact mode, 20 8 20 9 fast 3D single-particle tracking, 21 0 tapping mode, 20 9 21 0 Resolution, PFM studies, 20 7 20 8 RL cells, adhesion force. 127 – 128 conformation, 126 overview, 125 – 126 thermodynamics and structural parameters, 129 –130 trans association, 127 – 128 VE cells, see Vascular endothelial cells VIP receptor, mapping on osteoclasts,