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PDBsum entry 1d0t
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References listed in PDB file
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Key reference
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Title
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Phosphorothioate substitution can substantially alter RNA conformation.
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Authors
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J.S.Smith,
E.P.Nikonowicz.
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Ref.
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Biochemistry, 2000,
39,
5642-5652.
[DOI no: ]
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PubMed id
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Abstract
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Phosphorothioate substitution-interference experiments, routinely used to
stereospecifically identify phosphoryl oxygen sites that participate in
RNA-ligand binding and RNA-directed catalysis, rest in their interpretation on
the untested assumption that substitution does not alter the conformation of the
modified molecule from its biologically active state. Using NMR spectroscopy, we
have tested this assumption by determining the structural effect of
stereospecific phosphorothioate substitution at five positions in an RNA hairpin
containing the binding site for bacteriophage MS2 capsid protein. At most sites,
substitution has little or no effect, causing minor perturbations in the
phosphate backbone and increasing the stacking among nucleotides in the hairpin
loop. At one site, however, phosphorothioate substitution causes an unpaired
adenine necessary for formation of the capsid protein-RNA complex to loop out of
the RNA helix into the major groove. These results indicate that
phosphorothioate substitution can substantially alter the conformation of RNA at
positions of irregular secondary structure, complicating the use of
substitution-interference experiments to study RNA structure and function.
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Headers
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