Biological Applications of Dynamic Force Spectroscopy - Dynamic Force Spectroscopy and Biomolecular Recognition - page 193

6 Biological Applications

of Dynamic Force
Spectroscopy

Anna Rita Bizzarri and Salvatore Cannistraro

CONTENTS
6.1 Introduction................................................................................................... 193
6.2 Setup and Analysis Methods of DFS Experiments....................................... 196
6.2.1 Description of a DFS Experiment .................................................... 196
6.2.2 Analysis of the Force Curves ........................................................... 198
6.2.3 DFS and Computational Methods .................................................... 201
6.3 DFS Studies of Biomolecular Complexes .................................................... 201
6.3.1 A Paradigmatic Complex with Long Lifetime: Avidin-Biotin......... 202
6.3.2 DFS Studies of Antigen-Antibody Complexes................................ 207
6.3.3 DFS Studies of Complexes with Short Lifetime .............................. 212
6.3.4 DFS Studies of Complexes Involving DNA or Aptamers................ 219
6.3.5 DFS of Complexes Involved in Adhesion and
Aggregation Processes ..................................................................... 223
6.4 DFS-Based Biosensors and Other Applications ........................................... 231
6.5 Conclusions................................................................................................... 234
Acknowledgment ................................................................................................... 236
References.............................................................................................................. 236

6.1 INTRODUCTION
Interactions between biological molecules drive a large variety of cellular processes
and span a wide range of strengths and complexity. Upon specific recognition
mechanisms, biomolecules give rise to associations with different properties: from
antigen-antibody complexes characterized by tight binding, long lifetime, and high
specificity, to short-lived transient complexes involving molecules that recognize
multiple partners, sometimes with a charge transfer capability (Janin, 1997; Crowley
and Ubbink, 2003). The ability of biological molecules to undergo such highly con-
trolled and hierarchical processes is regulated by forces at molecular scale based on a
combination of noncovalent interactions (i.e., van der Waals, electrostatic, hydropho-
bic, hydrogen (H), and ionic bonds), which determine the strength and the charac-
teristic time of the complexes. More generally, the instructions driving molecules to

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