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Int. J. Mol. Sci. 2008, 9(3), 422-433; doi:10.3390/ijms9030422

Effect of Locked-Nucleic Acid on a Biologically Active G-Quadruplex. A Structure-Activity Relationship of the Thrombin Aptamer

1, 2 and 1,*
Received: 23 January 2008 / Revised: 17 March 2008 / Accepted: 18 March 2008 / Published: 24 March 2008
(This article belongs to the Special Issue Nucleic Acid Derivatives in Emerging Technologies)
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Here we tested the ability to augment the biological activity of the thrombin aptamer, d(GGTTGGTGTGGTTGG), by using locked nucleic acid (LNA) to influence its G-quadruplex structure. Compared to un-substituted control aptamer, LNA-containing aptamers displayed varying degrees of thrombin inhibition. Aptamers with LNA substituted in either positions G5, T7, or G8 showed decreased thrombin inhibition, whereas LNA at position G2 displayed activity comparable to un-substituted control aptamer. Interestingly, the thermal stability of the substituted aptamers does not correlate to activity – the more stable aptamers with LNA in position G5, T7, or G8 showed the least thrombin inhibition, while a less stable aptamer with LNA at G2 was as active as the un-substituted aptamer. These results suggest that LNA substitution at sites G5, T7, and G8 directly perturbs aptamer-thrombin affinity. This further implies that for the thrombin aptamer, activity is not dictated solely by the stability of the G-quadruplex structure, but by specific interactions between the central TGT loop and thrombin and that LNA can be tolerated in a biologically active nucleic acid structure albeit in a position dependent fashion.
Keywords: aptamer; G-quadruplex; thrombin; locked nucleic acid (LNA) aptamer; G-quadruplex; thrombin; locked nucleic acid (LNA)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Bonifacio, L.; Church, F.C.; Jarstfer, M.B. Effect of Locked-Nucleic Acid on a Biologically Active G-Quadruplex. A Structure-Activity Relationship of the Thrombin Aptamer. Int. J. Mol. Sci. 2008, 9, 422-433.

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