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6GZK

Solution NMR structure of the tetramethylrhodamine (TMR) aptamer 3 in complex with 5-TAMRA

Summary for 6GZK
Entry DOI10.2210/pdb6gzk/pdb
NMR InformationBMRB: 26842
DescriptorTMR3 (48-MER), 5-carboxy methylrhodamine (2 entities in total)
Functional Keywordsrna aptamer, rna-ligand complex, three-way junction, rna
Biological sourcesynthetic construct
Total number of polymer chains1
Total formula weight15925.69
Authors
Duchardt-Ferner, E.,Ohlenschlager, O.,Kreutz, C.R.,Wohnert, J. (deposition date: 2018-07-04, release date: 2019-07-17, Last modification date: 2024-05-15)
Primary citationDuchardt-Ferner, E.,Juen, M.,Bourgeois, B.,Madl, T.,Kreutz, C.,Ohlenschlager, O.,Wohnert, J.
Structure of an RNA aptamer in complex with the fluorophore tetramethylrhodamine.
Nucleic Acids Res., 48:949-961, 2020
Cited by
PubMed Abstract: RNA aptamers-artificially created RNAs with high affinity and selectivity for their target ligand generated from random sequence pools-are versatile tools in the fields of biotechnology and medicine. On a more fundamental level, they also further our general understanding of RNA-ligand interactions e. g. in regard to the relationship between structural complexity and ligand affinity and specificity, RNA structure and RNA folding. Detailed structural knowledge on a wide range of aptamer-ligand complexes is required to further our understanding of RNA-ligand interactions. Here, we present the atomic resolution structure of an RNA-aptamer binding to the fluorescent xanthene dye tetramethylrhodamine. The high resolution structure, solved by NMR-spectroscopy in solution, reveals binding features both common and different from the binding mode of other aptamers with affinity for ligands carrying planar aromatic ring systems such as the malachite green aptamer which binds to the tetramethylrhodamine related dye malachite green or the flavin mononucleotide aptamer.
PubMed: 31754719
DOI: 10.1093/nar/gkz1113
PDB entries with the same primary citation
Experimental method
SOLUTION NMR
Structure validation

238582

数据于2025-07-09公开中

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