Figure 7.

Binary Cy3 aptamer probe composed of folded modules (Endo & Nakamura 2010). (A) Optimized structure of Cy3apt. Ten nucleotides (white letters in black boxes) represent substitutions from the original Cy3apt sequence to optimize affinity to Cy3. ‘Δ3′GCG’ denotes a 3-base deletion on the 3′ end. ‘Tri-reversion’ indicates three bases that reverted to the original. (B) SPR sensorgrams of Cy3apt binding to Cy3 immobilized on the sensor chip. The indicated concentrations of RNAs were injected at time 0 for 30 s at a flow rate of 10 μL/min. (C) Binary Cy3 aptamer probe to detect target oligonucleotides. Schematic representation of the target oligonucleotide and the binary aptamer probe (I-bin and II-bin). The target oligonucleotide T2 sequence is shown, and the variable linker sequences are boxed. M2-1 and M2-2 are single nucleotide mismatches introduced into T2. Target-binding sequences of the binary probe are depicted as lowercase letters. (D) Detection of target oligonucleotides using the binary probe as SPR signals. Target oligonucleotides (10 μm) with (closed box) or without (open box) the binary probe (16 μm) were subjected to SPR analysis.