Riboswitches are RNA regulatory elements that perform regulation functions through conformational switch induced by specific binding of cognate metabolites.Nowadays, native structures have been determined for the ligand-free state of several riboswitches, which are similar to their bound state.Nevertheless, these bound-like in free-state conformations cant perform their corresponding functions.Investigations of the free state comparing with bound state will advance our understanding of RNA folding, ligand binding as well as the diverse regulation functions of riboswitches.Here we study the unfolding kinetics of two types of preQ1 aptamer domain with similar structure but totally different regulation functions through all-atom molecular dynamic simulation.It is found that these two types of preQ1 riboswitch have similar overall dynamic feature but different details.There exist different stable intermediates during the unfolding process of these preQl riboswitches, which may be related to their functions.The intermediate structures in bound state are good candidates for ligand binding, which will help the molecule to adopt their functional "Off" states with pseudoknot.While the intermediate states in absence of ligand have diverse conformations as their functional "On" states.Our results also indicate that the evolution and natural selection bring up the various lengths of L2 regions in different types of preQ 1 riboswitches that lead to the various regulation functions.These results may also be helpful to explain other types of riboswitches .