Chinese Journal of Magnetic Resonance ›› 2006, Vol. 23 ›› Issue (2): 161-168.

• Articles • Previous Articles     Next Articles

NMR Study  of the Unfolding Mechanism for the Thrombin-Binding  DNA Aptamer d (GGTTGGTGTGGTTGG)

  

  1. 1.State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics(Wuhan Institute of Physics and Mathematics,  the Chinese Academy of Sciences), Wuhan 430071, China; 
    2.Graduate School of The Chinese Academy Sciences, Beijing 100049, China
  • Received:2005-11-25 Revised:2006-01-17 Published:2006-06-05 Online:2006-06-05
  • Supported by:

    国家科技部(2002CB71386); 国家自然科学基金(10234070, 20475061, 20610104)资助项目.

Abstract:

15mer DNA  d(GGTTGGTGTGGTTGG) is a  thrombin-binding DNA aptamer (TBA), with inhibits clotting, of a high affinity with thrombin. In the presence of K+, TBA forms a right-handed-helix chair-like conformation with two stacked G-quartets and a regular phosphodiester backbone. The two G-quartets are linked by two TT loops at one end and a TGT loop at the other. The Hydrogen exchange rates of the imino protons of TBA in the presence of K+ were measured in this study. The results show that the G2, G11 and G15 iminos outside both the TGT loop and the two TT loops exchange faster, and in comparison the G6, G5 and G14 iminos have lower exchange rates because of the protection from the TGT loop and the TT loops. We also found that the stability of the TGT loop is similar to the two TT loops, and that the bases T4, T13 and T9 play more important roles in keeping the hydrogen bond stable in the K+: TBA complex than in the Sr2+: TBA complex. Evidence was obtained for the unfolding mechanism for the thrombin-binding aptamer. The data show that the hydrogen bonds between G2 and G14, G11 and G5, G15 and G1 outside the loops break first, and when the temperature increases further, the TGT loop and the two TT loops also become random coils.

Key words: NMR, unfolding mechanism , thrombin binding DNA aptamer, G-quadruplex, TGT loop, TT loop

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