The Spot-Nanobody (green) binds to the Spot-Tag sequence motif PDRVRAVSHWSS. Upon binding, the Spot-Tag peptide is embedded on the surface of the Spot-Nanobody and becomes a β-sheet extension of the Spot-VHH. Defined interactions of the Spot-Nanobody’s side chains to the Spot-peptide determine specificity. In addition, the Spot-peptide is clamped by two amino acid side chains of the Spot-Nanobody. This binding mechanism elucidates why the Spot-Nanobody binds with high affinity to the Spot-Tag.
You may have noticed the recent publication “A peptide tag-specific nanobody enables high-quality labeling for STORM imaging” of Virant et al (2018) in Nature Communications doi: 10.1038/s41467-018-03191-2, where for the first time a peptide-tag specific Nanobody was applied in dSTORM imaging: The authors have described and discussed the performance of a BC2 peptide-tag specific Nanobody to image BC2 peptide tag fusion proteins in super resolution microscopy, i.e. dSTORM. This Blog features that BC2 peptide-tag specific Nanobody, which ChromoTek markets under the names Spot-Label® and Spot-Trap®. In addition, this Blog figures the significantly improved version of the BC2 peptide -tag, which is called Spot-Tag®.