Factor IX (FIX) is an important protein in the blood clotting cascade, playing a key role. Previously, an anti-FIX RNA aptamer (34 mer) was generated to block blood coagulation, in order for it to be used as a substitute for currently available anti-coagulants. Bases in the loop region of this RNA aptamer have mainly involved the binding of FIX. Changes in 2 bases were found to diminish the complex formation with FIX, which could be predicted by evaluating the alteration in the secondary structure of the aptamer. In this study, computational analyses were carried out on the secondary structure analysis with aptamer, and the possible changes observed. It was confirmed that both A10 and A12 are the key bases involved in the complex formation with FIX. Similar structural analysis may helpful in identifying and predicting the importance of RNA bases in maintaining the secondary structure and their binding affinity.
