PHYSICAL LIMITS ON THE MECHANICAL MEASUREMENT OF THE SECONDARY STRUCTURE OF BIO-MOLECULES

The forces and lengths needed to mechanically denature a protein or nucleic acid are within the capabilities of the Atomic-Force Microscope. However, thermal fluctuations in the filament between the partially unfolded molecule and the force cantilever attenuate any measure of secondary structure on a length similar to (2/pi(2))(epsilon/k(B) T)(3/2) (aA)(1/2), where epsilon is the energy required to liberate a length a of filament whose persistence length is A. Hence individual base pairs cannot readily be resolved but the stem-loop structure of RNA should be.