Atomic Force Microscopy in Liquid: Biological Applications

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