We rationally designed a new inosine monophosphate (IMP) aptamer based on structural information from the natural thiamine pyrophosphate (TPP) riboswitch and an in vitro-selected hypoxanthine aptamer. The value of the binding affinity (K(a)) for the newly designed IMP aptamer for IMP was (2.6 +/- 3.2) x 10(7) M(-1), which was 10-times larger than that for TPP. These results demonstrated that structure-based design of aptamers can be a useful scheme to develop artificial aptamers.