1D0T

SOLUTION STRUCTURE OF A PHOSPHOROTHIOATE MODIFIED RNA BINDING SITE FOR PHAGE MS2 COAT PROTEIN

Summary for 1D0T

• Entry DOI: 10.2210/pdb1d0t/pdb
• Related: 1D0U
• Descriptor: PHOSPHOROTHIOATE SUBSTITUTED PHAGE MS2 RNA BINDING SITE (1 entity in total)
• Functional Keywords: rna hairpin, phosphorothioate, thiophosphate, bulged base, stem-loop, rna
• Total number of polymer chains: 1
• Total formula weight: 6809.38

Authors

Smith, J.S.,Nikonowicz, E.P. (deposition date: 1999-09-14, release date: 2000-05-24, Last modification date: 2024-05-22)

Primary citation

Smith, J.S.,Nikonowicz, E.P.
Phosphorothioate substitution can substantially alter RNA conformation.
Biochemistry, 39:5642-5652, 2000

PubMed Abstract: 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.

PubMed: 10801314
DOI: 10.1021/bi992712b

Experimental method

SOLUTION NMR