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Structure paper

TitleCo-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture.
Journal, issue, pagesNat Commun, Vol. 14, Page 2969-2969, Year 2023
Publish dateOct 28, 2022 (structure data deposition date)
AuthorsPassalacqua, L.F.M. / Starich, M.R. / Link, K.A. / Wu, J. / Knutson, J.R. / Tjandra, N. / Jaffrey, S.R. / Ferre-D'Amare, A.R.
External linksNat Commun / PubMed:37221204
MethodsX-ray diffraction
Resolution1.95 - 2.85 Å
Structure data

PDB-8eyu:
Structure of Beetroot dimer bound to DFAME
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-8eyv:
Structure of Beetroot dimer bound to DFHO
Method: X-RAY DIFFRACTION / Resolution: 2.55 Å

PDB-8eyw:
Beetroot dimer bound to ThT
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-8f0n:
Wobble Beetroot (A16U-U38G) dimer bound to DFHO
Method: X-RAY DIFFRACTION / Resolution: 2.85 Å

Chemicals

ChemComp-K:
Unknown entry

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

ChemComp-HOH:
WATER

ChemComp-747:
(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one

ChemComp-TFX:
2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium

Source
  • synthetic construct (others)
KeywordsRNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex

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