Disclosed herein are methods of screening candidate binding compounds to a plurality of target nucleic acids either of the same sequence or of different sequences utilizing a device configured to detect changes in the folding and unfolding force of the target nucleic acid upon binding to various candidate binding compounds. In the presence of a plurality of nucleic acid sequences, the methods described herein also can rapidly determine the specificity of the small molecule or polypeptide to a nucleic acid structure. Also, disclosed herein are methods of measuring binding kinetics of binding compounds to a target nucleic acid using a device configured to detect changes in the folding and unfolding force of the target nucleic acid upon binding to varying concentrations of the candidate binding compound.