Detecting Molecular Folding from Noise Measurements

Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We consider cases where Brownian force fluctuations are large, masking the force rips and jumps characteristics of conformational transitions. We compare unfolding and folding data for DNA hairpin systems of loop sizes 4, 8, and 20 and the 110-amino acid protein barnase, finding conditions that facilitate the detection of folding events at low forces where the signal-to-noise ratio is low. In particular, we discuss the role of temperature as a useful parameter to improve the detection of folding transitions in entropically driven processes where folding forces are temperature independent. The force variance approach might be extended to detect the elusive intermediate states in RNA and protein folding.