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. Author manuscript; available in PMC: 2009 Sep 15.
Published in final edited form as: Anal Biochem. 2008 May 20;380(2):164–173. doi: 10.1016/j.ab.2008.05.018

Figure 1.

Figure 1

Sequence and secondary structure of a designed conformation-switching anti-thrombin aptamer. (A) Inactive conformation in the absence of thrombin. The 3′ end of the aptamer has been extended with an antisense sequence (blue) in order to promote the formation of duplex structure and denaturation of the aptamer. (B) Active conformation in the presence of thrombin. Formation of a quadruplex and binding to thrombin stabilizes a structure in which the extended 3′ end of the aptamer (red) forms a short hairpin structure that can hybridize to a substrate oligonucleotide (green) to form a ligation junction. Following ligation with T4 DNA ligase, the ligated aptamer and substrate can be amplified by PCR using indicated forward (For) and reverse (Rev) primers. The position of the TaqMan MGB probe (Probe) used during real-time PCR amplification is indicated by a dashed red line. The sequence shown is aptamer ThrA7, which is further described in Figure 4a.