Binding of a Designed Anti-Cancer Drug to the Central Cavity of an RNA Three-Way Junction
Binding of a Designed Anti-Cancer Drug to the Central Cavity of an RNA Three-Way Junction
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DOI：
10.1002/anie.201305079
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发表时间：
2013-10-25
影响因子：
16.6
通讯作者：
Freisinger, Eva
中科院分区：
文献类型：
--
作者：
Phongtongpasuk, Siriporn;Paulus, Susann;Freisinger, Eva
Nucleic acids are exciting biomolecular targets because they offer the potential to regulate information transfer at the beginning, before the genetic code is translated into proteins. Metal complexes that bind to DNA have been of particular interest, with the cationic charge that metals impart being particularly attractive for recognition of these polyanions.[1] Examples include complexes that coordinate to the bases,[2] intercalate,[3] or bind to the phosphate backbone [4] of regular duplex DNA or, more recently, that recognize less common DNA structures such as bulges,[5] quadruplexes,[6] or junctions.[7] Such complexes have been explored as therapeutic drugs,[2] fluorescent imaging agents,[8] footprinting agents,[9] and for nanotechnology applications.[10] RNA binding by metal complexes is much less well understood.[11] Yet, RNA is an emerging biomedical target because its high structural diversity makes it highly suitable for supramolecular recognition. For example, a Diels–Alderase ribozyme was developed by invitro selection [12] and riboswitches have evolved naturally that are key to bacterial gene regulation. Both types of functional RNAs depend on specific ligand binding, for example, to a three-way junction (3WJ)-type cage as in the Diels–Alderase and the purine riboswitch,[13] with subsequent structural rearrangement.Hannon, Coll, and co-workers described the binding of a nano-sized dimetallic metal complex (a metallo-supramolecular cylinder) to the central cavity of a DNA 3WJ.[7a] Given that junctions are common in RNA structures, their recognition seemed an attractive initial step towards RNA structural recognition agents. Herein, we report the ability of a di-iron (II) supramolecular cylinder to recognize an RNA 3WJ and use X-ray crystallography to characterize the binding mode. While there are some crystal structures of RNAs with simple hexaqua or hexammine cations,[14] to the best of our knowledge this is the first crystallographic study of a designed metal complex bound to RNA. We first crystallized the di-iron (II) supramolecular cylinder with a palindromic RNA hexanucleotide sequence (Figure 1 A), which was selected to allow a direct comparison with the structure of the analogous DNA in complex with the cylinder.[7a, c, d] Crystals diffracting to 1.91 were obtained under similar crystallization conditions and contain exclusively the M enantiomer of the cylinder. The structure reveals an RNA 3WJ with the cylinder sitting at the heart of the junction (Figure 1 B). Additional cylinder molecules reside at the GC termini of the duplex RNA arms that radiate from the junction, with the bases making p-stacking interactions with the cylinder phenylene rings forming what is in effect an additional non-covalent pseudo-junction. While the overall structure obtained is highly similar to the one of the DNA 3WJ, distinct differences exist in the mode of recognition of the cylinder by the RNA 3WJ. These variations mainly originate from the specific conformation of the DNA versus the RNA oligonucleotide. Whereas the double-stranded parts of the DNA in the 3WJ adopt a B-form, the RNA shows its usual A-form. Overall, the DNA 3WJ resembles a truncated cone (Figure 1C) with a narrower top being formed by the 3’ends (Figure 2A), while the 5’ends point away from the central opening. The top and bottom openings of the RNA 3WJ are more similar in size (Figure 1B) with the 3’and 5’ends bent away from the central opening, effectively side-stepping any interaction with the cylinder. Accordingly, the narrowest part of the RNA junction is formed by the central adenine and uracil bases. In the DNA 3WJ, two main interactions with the cylinder are described: 1) the …
