DSSR-derived G-quadruplex features in PDB entry 4ts2
- X-ray (2.88 Å)
- Crystal structure of the spinach RNA aptamer in complex with dfhbi, magnesium ions
- Warner, K.D., Chen, M.C., Song, W., Strack, R.L., Thorn, A., Jaffrey, S.R., Ferre-D'Amare, A.R.: (2014) "Structural basis for activity of highly efficient RNA mimics of green fluorescent protein." Nat.Struct.Mol.Biol., 21, 658-663.
- GFP and its derivatives revolutionized the study of proteins. Spinach is a recently reported in vitro-evolved RNA mimic of GFP, which as genetically encoded fusions makes possible live-cell, real-time imaging of biological RNAs without resorting to large RNA-binding protein-GFP fusions. To elucidate the molecular basis of Spinach fluorescence, we solved the cocrystal structure of Spinach bound to its cognate exogenous chromophore, showing that Spinach activates the small molecule by immobilizing it between a base triple, a G-quadruplex and an unpaired G. Mutational and NMR analyses indicate that the G-quadruplex is essential for Spinach fluorescence, is also present in other fluorogenic RNAs and may represent a general strategy for RNAs to induce fluorescence of chromophores. The structure guided the design of a miniaturized 'Baby Spinach', and it provides a foundation for structure-driven design and tuning of fluorescent RNAs.
- G4 notes
- 2 G-tetrads, 1 G4 helix, 1 G4 stem · (2+2), UUDD
1 glyco-bond=--s- groove=-wn- planarity=0.335 type=other nts=4 GGGG X.G25,X.G29,Y.G72,Y.G68 2 glyco-bond=--ss groove=-w-n planarity=0.180 type=other nts=4 GGGG X.G26,X.G30,Y.G70,Y.G65
In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.
Helix#1, 2 G-tetrad layers, inter-molecular, with 1 stem
In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.