Recognition of Planar and Nonplanar Ligands in the Malachite Green-RNA Aptamer Complex

Ribonucleic acids are an attractive drug target owing to their central role in many pathological processes. Notwithstanding this potential, RNA has only rarely been successfully targeted with novel drugs. The difficulty of targeting RNA is at least in part due to the unusual mode of binding found in...

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Published in:Chembiochem : a European journal of chemical biology 2004-01, Vol.5 (1), p.62-72
Main Authors: Flinders, Jeremy, DeFina, Steven C, Brackett, David M, Baugh, Chris, Wilson, Charles, Dieckmann, Thorsten
Format: Article
Language:English
Subjects:
aptamers
Coloring Agents - chemistry
Crystallography, X-Ray
electrostatic interactions
ligand-RNA interactions
Ligands
Magnetic Resonance Spectroscopy
Malachite green
Models, Molecular
Mutation
NMR spectroscopy
Nucleic Acid Conformation
RNA - chemistry
RNA - genetics
RNA structures
Rosaniline Dyes - chemistry
Solutions
stacking interactions
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Summary:Ribonucleic acids are an attractive drug target owing to their central role in many pathological processes. Notwithstanding this potential, RNA has only rarely been successfully targeted with novel drugs. The difficulty of targeting RNA is at least in part due to the unusual mode of binding found in most small-molecule-RNA complexes: the ligand binding pocket of the RNA is largely unstructured in the absence of ligand and forms a defined structure only with the ligand acting as scaffold for folding. Moreover, electrostatic interactions between RNA and ligand can also induce significant changes in the ligand structure due to the polyanionic nature of the RNA. Aptamers are ideal model systems to study these kinds of interactions owing to their small size and the ease with which they can be evolved to recognize a large variety of different ligands. Here we present the solution structure of an RNA aptamer that binds triphenyl dyes in complex with malachite green and compare it with a previously determined crystal structure of a complex formed with tetramethylrosamine. The structures illustrate how the same RNA binding pocket can adapt to accommodate both planar and nonplanar ligands. Binding studies with single- and double-substitution mutant aptamers are used to correlate three-dimensional structure with complex stability. The two RNA-ligand complex structures allow a discussion of structural changes that have been observed in the ligand in the context of the overall complex structure. Base pairing and stacking interactions within the RNA fold the phosphate backbone into a structure that results in an asymmetric charge distribution within the binding pocket that forces the ligand to adapt through a redistribution of the positive partial charge.
ISSN:1439-4227
1439-7633
1439-4227
DOI:10.1002/cbic.200300701