Common applications of force spectroscopy are measurements of polymer elasticity, especially biopolymers such as RNA and DNA. Another biophysical application of polymer force spectroscopy is on protein unfolding. Modular proteins can be adsorbed to a gold or (more rarely) mica surface and then stretched. The sequential unfolding of modules is observed as a very characteristic sawtooth pattern of the force vs elongation graph; every tooth corresponds to the unfolding of a single protein module (apart from the last that is generally the detachment of the protein molecule from the tip). Much information about protein elasticity and protein unfolding can be obtained by this technique. Many proteins in the living cell must face mechanical stress.
Moreover, force spectroscopy can be used to investigate the enzymatic activity of proteins involved in DNA replication, transcription, organization and repair. This is achieved by measuring the position of a bead attached to a DNA-protein complex stalled on a DNA tether that has one end attached to a surface, while keeping the force constant. This technique has been used, for example, to study transcription elongation inhibition by Klebsidin and Acinetodin.
The other main application of force spectroscopy is the study of mechanical resistance of chemical bonds. In this case, generally the tip is functionalized with a ligand that binds to another molecule bound to the surface. The tip is pushed on the surface, allowing for contact between the two molecules, and then retracted until the newly formed bond breaks up. The force at which the bond breaks up is measured. Since mechanical breaking is a kinetic, stochastic process, the breaking force is not an absolute parameter, but it is a function of both temperature and pulling speed. Low temperatures and high pulling speeds correspond to higher breaking forces. By careful analysis of the breaking force at various pulling speeds, it is possible to map the energy landscape of the chemical bond under mechanical force. This is leading to interesting results in the study of antibody-antigen, protein-protein, protein-living cell interaction and catch bonds.
Recently this technique has been used in cell biology to measure the aggregative stochastic forces created by motor proteins that influence the motion of particles within the cytoplasm. In this way, force spectrum microscopy may be used better to understand the many cellular processes that require the motion of particles within cytoplasm.