posted on 2023-12-07, 15:11authored byYu Zhang, Xingru Fang, Wenwen Huang, Qi Li, Fan Hu, Honglin Liu
Decrypting
the in situ three-dimensional spatial
configuration of an aptamer is of considerable significance; however,
suitable nanoscale resolution tools are lacking. Herein, we show that
a new nanometal surface energy transfer (NSET) optical nanoruler has
a record resolution, down to single-nucleobase levels. We labeled
fluorophores on different T bases of XQ-2d, including 5′, 3′,
6T, 22T, 38T, and 52T positions. The NSET nanoruler in situ decrypted the base sequence-dependent distance projection on the
nanogold surface, demonstrating that 5′, 3′, stem, and
loop structures are symmetrical in three-dimensional spatial configuration.
The orientation of the 5′ and 3′ stem was toward the
antiCD71-binding site, whereas the loop was in the opposite direction
at a considerable distance. Molecular docking simulation was performed
to list all of the possible conformations; however, all base distance
parameters projecting on the nanogold surface determined a single
conformation of XQ-2d. The specific binding sites of XQ-2d were Lys477,
Ser691, and Arg698 on the CD71 receptor.