Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Intricate 3D architecture of a DNA mimic of GFP.
Journal, issue, pages	Nature, Vol. 618, Issue 7967, Page 1078-1084, Year 2023
Publish date	Jun 21, 2023
Authors	Luiz F M Passalacqua / Michael T Banco / Jared D Moon / Xing Li / Samie R Jaffrey / Adrian R Ferré-D'Amaré /
PubMed Abstract	Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated ...Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates conditional fluorophores derived from GFP. To extend previous structural studies of fluorogenic RNAs, GFP and other fluorescent proteins to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.
External links	Nature / PubMed:37344591 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.5 - 6.5 Å
Structure data	EMDB-29329: Cryo-EM map of the unliganded Lettuce aptamer Method: EM (single particle) / Resolution: 6.5 Å PDB-8fhv: Structure of Lettuce aptamer bound to DFHBI-1T with thallium I ions Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-8fhx: Structure of Lettuce aptamer bound to DFHBI-1T Method: X-RAY DIFFRACTION / Resolution: 2.5 Å PDB-8fhz: Structure of Lettuce aptamer bound to DFHO Method: X-RAY DIFFRACTION / Resolution: 2.6 Å PDB-8fi0: Structure of Lettuce aptamer bound to DFAME Method: X-RAY DIFFRACTION / Resolution: 3 Å PDB-8fi1: Structure of Lettuce C20G bound to DFHO Method: X-RAY DIFFRACTION / Resolution: 2.6 Å PDB-8fi2: Structure of Lettuce C20T bound to DFHBI-1T Method: X-RAY DIFFRACTION / Resolution: 3 Å PDB-8fi7: Structure of Lettuce C20T bound to DFHO Method: X-RAY DIFFRACTION / Resolution: 2.9 Å PDB-8fi8: Structure of Lettuce C20T bound to DFAME Method: X-RAY DIFFRACTION / Resolution: 2.8 Å
Chemicals	ChemComp-TL: THALLIUM (I) ION ChemComp-MG: Unknown entry ChemComp-2ZY: (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one ChemComp-HOH: WATER ChemComp-K: Unknown entry ChemComp-747: (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one ChemComp-X5R: methyl (2E)-3-{(4Z)-4-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-1-methyl-5-oxo-4,5-dihydro-1H-imidazol-2-yl}prop-2-enoate
Source	synthetic construct (others)
Keywords	DNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex