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• W2131457029 endingPage "128" @default.
• W2131457029 startingPage "117" @default.
• W2131457029 abstract "Previous in vitro selection experiments identified an RNA aptamer that recognizes the chromophore malachite green (MG) with a high level of affinity, and which undergoes site-specific cleavage following laser irradiation. To understand the mechanism by which this RNA folds to recognize specifically its ligand and the structural basis for chromophore-assisted laser inactivation, we have determined the 2.8 A crystal structure of the aptamer bound to tetramethylrosamine (TMR), a high-affinity MG analog. The ligand-binding site is defined by an asymmetric internal loop, flanked by a pair of helices. A U-turn and several non-canonical base interactions stabilize the folding of loop nucleotides around the TMR. The aptamer utilizes several tiers of stacked nucleotides arranged in pairs, triples, and a novel base quadruple to effectively encapsulate the ligand. Even in the absence of specific stabilizing hydrogen bonds, discrimination between related fluorophores and chromophores is possible due to tight packing in the RNA binding pocket, which severely limits the size and shape of recognized ligands. The site of laser-induced cleavage lies relatively far from the bound TMR ( approximately 15 A). The unusual backbone conformation of the cleavage site nucleotide and its high level of solvent accessibility may combine to allow preferential reaction with freely diffusing hydroxyl radicals generated at the bound ligand. Several observations, however, favor alternative mechanisms for cleavage, such as conformational changes in the aptamer or long-range electron transfer between the bound ligand and the cleavage site nucleotide." @default.
• W2131457029 created "2016-06-24" @default.
• W2131457029 creator A5013113898 @default.
• W2131457029 creator A5042505758 @default.
• W2131457029 creator A5065718203 @default.
• W2131457029 date "2000-08-01" @default.
• W2131457029 modified "2023-10-16" @default.
• W2131457029 title "2.8 Å crystal structure of the malachite green aptamer 1 1Edited by J. A. Doudna" @default.
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• W2131457029 doi "https://doi.org/10.1006/jmbi.2000.3951" @default.
• W2131457029 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/10926496" @default.
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