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The use of conformationally rigid nucleoside probes to study the role of sugar pucker and nucleobase orientation in the thrombin binding aptamer

  1. Author:
    Saneyoshi, H.
    Mazzini, S.
    Avino, A.
    Portella, G.
    Gonzalez, C.
    Orozco, M.
    Marquez, V. E.
    Eritja, R.

  2. Author Address

    Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, USA.
    1. Year: 2009
    2. Epub Date: 9/15/2009
  2. Journal: Nucleic acids symposium series (2004)
    1. 53
    2. Pages: 109-10
  4. Type of Article: Article
  5. ISSN: 1746-8272 (Electronic);0261-3166 (Linking)
  1. Abstract:

    Thrombin binding aptamers (TBAs) incorporating North-/South-deoxyguanosines built on the rigid bicyclo[3.1.0]hexane template were synthesized. Individual 2'-deoxyguanosines at positions dG14 and dG15 of the aptamer were replaced by these analogues where the North/anti and South/syn conformational states were confined. The substitution at position 14 with a locked South/syn-dG nucleoside produced an aptamer with the same stability and global structure as the innate, unmodified one. Replacing position 15 with the same South/syndG nucleoside induced a strong destabilization of the aptamer, while the antipodal North/anti-dG nucleoside was less destabilizing. Remarkably, the insertion of a North/anti-dG nucleoside at position 14, where both pseudosugar conformation and glycosyl torsion angle are opposite with respect to the native structure, led to the complete disruption of the G-tetraplex structure as detected by NMR and confirmed by extensive molecular dynamics simulations.

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  2. DOI: 10.1093/nass/nrp055
  3. PMID: 19749284

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