5NS4
Crystal structures of Cy3 cyanine fluorophores stacked onto the end of double-stranded RNA
Summary for 5NS4
| Entry DOI | 10.2210/pdb5ns4/pdb |
| Descriptor | 50S ribosomal protein L5, RNA (34-MER), MAGNESIUM ION, ... (5 entities in total) |
| Functional Keywords | cy3, fluorophores, rna, rna binding protein |
| Biological source | Thermus thermophilus More |
| Total number of polymer chains | 4 |
| Total formula weight | 62852.34 |
| Authors | Liu, Y.J.,Lilley, D.M.J. (deposition date: 2017-04-25, release date: 2017-12-20, Last modification date: 2024-01-17) |
| Primary citation | Liu, Y.,Lilley, D.M.J. Crystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA. Biophys. J., 113:2336-2343, 2017 Cited by PubMed Abstract: The indodicarbocyanine fluorophores Cy3 and Cy5 are extensively used as donor-acceptor pairs in fluorescence resonance energy transfer experiments, especially those involving single molecules. When terminally attached to double-stranded nucleic acids via the 5' phosphate group these fluorophores stack onto the ends of the molecule. Knowledge of the positions of the fluorophores is critical to the interpretation of fluorescence resonance energy transfer data. The positions have been demonstrated for double-stranded (ds) DNA using NMR spectroscopy. Here, we have used x-ray crystallography to analyze the location of Cy3 and Cy5 on dsRNA, using complexes of an RNA stem-loop bound to L5 protein determined at 2.4 Å resolution. This confirms the tendency of both fluorophores to stack on the free end of RNA, with the long axis of the fluorophores approximately parallel to that of the terminal basepair. However, the manner of interaction of both Cy3 and Cy5 with the terminus of the dsRNA is significantly different from that deduced for dsDNA using NMR. The fluorophores are stacked on the terminal basepair such that their indole nitrogen atoms lie on the major groove side, and thus their pendant methyl groups are on the minor groove side. PubMed: 29211987DOI: 10.1016/j.bpj.2017.10.002 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.4 Å) |
Structure validation
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