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1RDE

NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+

Summary for 1RDE
Entry DOI10.2210/pdb1rde/pdb
NMR InformationBMRB: 6009
DescriptorThrombin-binding DNA aptamer (1 entity in total)
Functional Keywordsthrombin-binding dna, sr2+, quadruplex, dna
Total number of polymer chains1
Total formula weight4743.05
Authors
Mao, X.,Marky, L.A.,Gmeiner, W.H. (deposition date: 2003-11-05, release date: 2003-11-11, Last modification date: 2024-05-22)
Primary citationMao, X.,Marky, L.A.,Gmeiner, W.H.
NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+.
J.Biomol.Struct.Dyn., 22:25-33, 2004
Cited by
PubMed Abstract: The structure of thrombin-binding DNA aptamer complexed with a single Sr2+ ion (Sr2+:TBA complex) has been determined using NMR spectroscopy and restrained molecular dynamics simulations. The quadruplex structure for the Sr2+:TBA complex is similar in topology, but distinct in structure, from that previously reported for the K+:TBA complex. The inter-tetrad distance of the Sr2+:TBA complex is 3.8 angstroms, or 0.7 angstroms larger than in the K+:TBA complex. This substantial difference can be attributed to a different binding site for Sr2+ in the Sr2+:TBA complex than for K+ in the K+:TBA complex. The Sr2+:TBA complex assumes a 1:1 stoichiometry, and it is very likely that the Sr2+ ion simultaneously interacts with the eight O6 atoms of the two G-tetrads. The results indicate that quadruplex DNA structures are highly sensitive to the presence of specific metal ions. The binding of specific metal ions may modulate the biological activity of quadruplex DNA structures in vivo.
PubMed: 15214802
PDB entries with the same primary citation
Experimental method
SOLUTION NMR
Structure validation

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