6V9B

Co-crystal structure of the fluorogenic Mango-IV homodimer bound to TO1-Biotin

Summary for 6V9B

• Entry DOI: 10.2210/pdb6v9b/pdb
• Descriptor: RNA (28-MER), ~{N}-methyl-2-[2-[(~{E})-(1-methylquinolin-4-ylidene)methyl]-1,3-benzothiazol-3-yl]ethanamide, POTASSIUM ION (3 entities in total)
• Functional Keywords: rna, aptamer, fluorescence
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 19710.91

Authors

Trachman, R.J.,Ferre-D'Amare, A.R. (deposition date: 2019-12-13, release date: 2020-05-20, Last modification date: 2024-03-06)

Primary citation

Trachman 3rd, R.J.,Cojocaru, R.,Wu, D.,Piszczek, G.,Ryckelynck, M.,Unrau, P.J.,Ferre-D'Amare, A.R.
Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair.
Structure, 28:776-785.e3, 2020

PubMed Abstract: Fluorescent RNA aptamers have been used in cells as biosensor reporters and tags for tracking transcripts. Recently, combined SELEX and microfluidic fluorescence sorting yielded three aptamers that activate fluorescence of TO1-Biotin: Mango-II, Mango-III, and Mango-IV. Of these, Mango-IV was best at imaging RNAs in both fixed and live mammalian cells. To understand how Mango-IV achieves activity in cells, we determined its crystal structure complexed with TO1-Biotin. The structure reveals a domain-swapped homodimer with two independent G-quadruplex fluorophore binding pockets. Structure-based analyses indicate that the Mango-IV core has relaxed fluorophore specificity, and a tendency to reorganize binding pocket residues. These molecular properties may endow it with robustness in the cellular milieu. Based on the domain-swapped structure, heterodimers between Mango-IV and the fluorescent aptamer iSpinach, joined by Watson-Crick base pairing, were constructed. These exhibited FRET between their respective aptamer-activated fluorophores, advancing fluorescent aptamer technology toward multi-color, RNA-based imaging of RNA coexpression and colocalization.

PubMed: 32386573
DOI: 10.1016/j.str.2020.04.007

Experimental method

X-RAY DIFFRACTION (2.4 Å)