Computational Base Substitution Analyses on Secondary Structure of Aptamer: Conformational Changes Diminish Complex Formation


  • Thangavel LAKSHMIPRIYA Advanced Medical & Dental Institute, Universiti Sains Malaysia, Kepala Batas, Penang
  • Subash Chandra Bose GOPINATH School of Bioprocess Engineering, Universiti Malaysia Perlis, 02600 Arau, Perlis
  • Uda HASHIM Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, 01000 Kangar, Perlis
  • Suresh Venkata CHINNI Department of Biotechnology, Faculty of Applied Sciences AIMST University, 08100 Bedong
  • Thean-Hock TANG Advanced Medical & Dental Institute, Universiti Sains Malaysia, Kepala Batas, Penang



BayesFold, mfold, aptamer, factor IX, secondary structure


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.


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How to Cite

LAKSHMIPRIYA, T., GOPINATH, S. C. B., HASHIM, U., CHINNI, S. V., & TANG, T.-H. (2018). Computational Base Substitution Analyses on Secondary Structure of Aptamer: Conformational Changes Diminish Complex Formation. Walailak Journal of Science and Technology (WJST), 15(9), 645–657.



Research Article