Atomic Force Microscopy in Liquid: Biological Applications

About 40 % of current atomic force microscopy (AFM) research is performed in liquids, making liquid–based AFM a rapidly growing and important tool for the study of biological materials. This book focuses on the underlying principles and experimental aspects of AFM under liquid, with an easy–to–follow organization intended for new AFM scientists. The book also serves as an up–to–date review of new AFM techniques developed especially for biological samples. Aimed at physicists, materials scientists, biologists, analytical chemists, and medicinal chemists. An ideal reference book for libraries. From the contents: Part I: General Atomic Force Microscopy ∗ AFM: Basic Concepts ∗ Carbon Nanotube Tips in Atomic Force Microscopy with ∗ Applications to Imaging in Liquid ∗ Force Spectroscopy ∗ Atomic Force Microscopy in Liquid ∗ Fundamentals of AFM Cantilever Dynamics in Liquid ∗ Environments ∗ Single–Molecule Force Spectroscopy ∗ High–Speed AFM for Observing Dynamic Processes in Liquid ∗ Integration of AFM with Optical Microscopy Techniques Part II: Biological Applications ∗ DNA and Protein–DNA Complexes ∗ Single–Molecule Force Microscopy of Cellular Sensors ∗ AFM–Based Single–Cell Force Spectroscopy ∗ Nano–Surgical Manipulation of Living Cells with the AFM

PART I: General Atomic Force Microscopy AFM: BASIC CONCEPTS Atomic Force Microscope: Principles Piezoelectric Scanners Tips and Cantilevers Force Detection Methods for Imaging in Liquids AFM Operation Modes: Contact, Jumping/Pulsed, Dynamic The Feedback Loop Image Representation Artifacts and Resolution Limits CARBON NANOTUBE TIPS IN ATOMIC FORCE MICROSCOPY WITH APPLICATIONS TO IMAGING IN LIQUID Introduction Fabrication of CNT AFM Probes Chemical Functionalization Mechanical Properties of CNTs in Relation to AFM Applications Dynamics of CNT Tips in Liquid Performance and Resolution of CNT Tips in Liquid FORCE SPECTROSCOPY Introduction Measurement of Force Curves Measuring Surface Forces by the Surface Force Apparatus Forces between Macroscopic Bodies Theory of DLVO Forces between Two Surfaces Van der Waals Forces – the Hamaker Constant Electrostatic Force between Surfaces in a Liquid Spatially Resolved Force Spectroscopy Force Spectroscopy Imaging of Single DNA Molecules Solvation Forces Hydrophobic Forces Steric Forces Conclusive Remarks DYNAMIC–MODE AFM IN LIQUID Introduction Operation Principles Instrumentation Quantitative Force Measurements High–Resolution Imaging Summary and Future Prospects FUNDAMENTALS OF AFM CANTILEVER DYNAMICS IN LIQUID ENVIRONMENTS Introduction Review of Fundamentals of Cantilever Oscillation Hydrodynamics of Cantilevers in Liquids Methods of Dynamic Excitation Dynamics of Cantilevers Interacting with Samples in Liquids Outlook SINGLE–MOLECULE FORCE SPECTROSCOPY Introduction AFM–SMFS Principles Dynamics of Adhesion Bonds Specific versus Other Interactions Steered Molecular Dynamics Simulations Biological Findings Using AFM–SMFS Concluding Remarks HIGH–SPEED AFM FOR OBSERVING DYNAMIC PROCESSES IN LIQUID Introduction Theoretical Derivation of Imaging Rate and Feedback Bandwidth Techniques Realizing High–Speed Bio–AFM Substrate Surfaces Imaging of Dynamic Molecular Processes Future Prospects of High–Speed AFM Conclusion INTEGRATION OF AFM WITH OPTICAL MICROSCOPY TECHNIQUES Introduction Combining AFM and IRM–TIRF Combining AFM and FRET FRET–AFM Sample Preparation and Experiment Setup PART II: Biological Applications AFM IMAGING IN LIQUID OF DNA AND PROTEIN–DNA COMPLEXES Overview: the Study of DNA at Nanoscale Resolution Sample Preparation for AFM Imaging of DNA and Protein–DNA Complexes AFM of DNA in Aqueous Solutions AFM Imaging of Alternative DNA Conformations Dynamics of Protein – DNA Interactions DNA Condensation Conclusions STABILITY OF LIPID BILAYERS AS MODEL MEMBRANES: ATOMIC FORCE MICROSCOPY AND SPECTROSCOPY APPROACH Biological Membranes Mechanical Characterization of Lipid Membranes Future Perspectives SINGLE–MOLECULE ATOMIC FORCE MICROSCOPY OF CELLULAR SENSORS Introduction Methods Probing Single Yeast Sensors in Live Cells Conclusions A FM–BASED SINGLE–CELL FORCE SPECTROSCOPY Introduction Cantilever Choice Cantilever Functionalization Cantilever Calibration Cell Attachment to the AFM Cantilever Recording a Force – Distance Curve Processing F – D Curves Quantifying Overall Cell Adhesion by SCFS SFCS with Single–Molecule Resolution Dynamic Force Spectroscopy Measuring Cell – Cell Adhesion Conclusions and Outlook NANOSURGICAL MANIPULATION OF LIVING CELLS WITH THE AFM Introduction: Mechanical Manipulation of Living Cells Basic Mechanical Properties of Proteins and Cells Hole Formation on the Cell Membrane Extraction of mRNA from Living Cells DNA Delivery and Gene Expression Mechanical Manipulation of Intracellular SFs Cellular Adaptation to Local Stresses Application of Carbon Nanotube Needles Use of Fabricated AFM Probes with a Hooking Function Membrane Protein Extraction Future Prospects

Arturo M Baro has spent most of his career at the Universidad Autonoma of Madrid and has been working in the fi eld of Surface Physics and Nanoscience. In 1983, he spent one year at the IBM Research Lab in Zürich where he worked with Professors Rohrer and Binnig, who discovered STM. He is the author of 160 publications with a citation index h = 38. In 1985, he founded the company NANOTEC ELECTRONICA, S.L., which is dedicated to the fabrication and sale of AFM machines. He has been honored with the research prizes from the Humboldt Foundation. Ronald G. Reifenberger has been on the faculty at Purdue University, W. Lafayette, USA since 1978. Following his PhD in physics from the University of Chicago, he was a post–doctoral fellow at the University of Toronto, Canada. His nanophysics laboratory at Purdue uses innovative experimental techniques to examine nanoscale properties of matter. His research focus since 1985 has been primarily scanning probe microscopy. Reifenberger is currently the director of the Kevin G. Hall Nanometrology Laboratory in the Birck Nanotechnology Center at Purdue.