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Record Resolution of Nanometal Surface Energy Transfer Optical Nanoruler Projects 3D Spatial Configuration of Aptamers on a Living Cell Membrane
journal contributionposted on 2023-12-07, 15:11 authored by Yu 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.
molecular docking simulationdimensional spatial configurationspecific binding sitesdependent distance projection3 ′ stemnanogold surface determinednanogold surfaceconsiderable distancebinding site5 ′situ record resolutionpossible conformationsoptical nanoruleropposite directionnucleobase levelslabeled fluorophoresconsiderable significancecd71 receptorbase sequence52t positions