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. 2021 Jun 25;49(20):11407–11424. doi: 10.1093/nar/gkab515

Figure 2.

Figure 2.

Presumed secondary structures of the optimized UB-DNA aptamers that bind specifically to each DEN-NS1 serotype. AptD1 (D1-1-48h) binds to DEN1-NS1 (variant 1), AptD2 (D2-1d-72h) to DEN2-NS1 (variant 1), AptD3 (D3-2-59h) to DEN3-NS1, and AptD4 (D4-3-57h) to DEN4-NS1. All aptamers contain two Ds bases, while AptD2 contains one Pa and two Ds bases, which are essential for tight binding to the target. The Ds and Pa bases are shown in red with yellow and pink circles, respectively. AptD2 has several G-tract regions, shown in bold, and the four G-tract regions in blue are involved in the G-quadruplex formation. The sequences in the random region and the constant primer regions are shown with light-blue and light-green circles, respectively, and the sequences intentionally mutated to stabilize base pairing are shown in red. The mini-hairpin DNA sequences, CGCGTAGCG, are shown in red with orange circles. The thymidines within the mini-hairpin DNA sequences are used as the biotinylation sites.