AI Article Synopsis
- The study focuses on improving the understanding of an aptamer's three-dimensional structure, which is currently hindered by a lack of precise measurement tools.
- Researchers developed a new optical tool called the nanometal surface energy transfer (NSET) nanoruler, achieving unprecedented resolution down to single nucleobases for this task.
- They found that the structure of the aptamer XQ-2d is symmetrical and that specific bases align in particular orientations towards the CD71 receptor's binding sites, highlighting its unique conformational properties.
Article Abstract
Decrypting the 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 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.
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| http://dx.doi.org/10.1021/acs.nanolett.3c04322 | DOI Listing |
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