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PDBsum entry 1d0t
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DOI no:
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Biochemistry
39:5642-5652
(2000)
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PubMed id:
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Phosphorothioate substitution can substantially alter RNA conformation.
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J.S.Smith,
E.P.Nikonowicz.
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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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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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A.Schwartz,
M.Rabhi,
F.Jacquinot,
E.Margeat,
A.R.Rahmouni,
and
M.Boudvillain
(2009).
A stepwise 2'-hydroxyl activation mechanism for the bacterial transcription termination factor Rho helicase.
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Nat Struct Mol Biol,
16,
1309-1316.
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T.Mashima,
A.Matsugami,
F.Nishikawa,
S.Nishikawa,
and
M.Katahira
(2009).
Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein.
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Nucleic Acids Res,
37,
6249-6258.
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PDB code:
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A.Matsugami,
T.Ohyama,
M.Inada,
N.Inoue,
N.Minakawa,
A.Matsuda,
and
M.Katahira
(2008).
Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance.
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Nucleic Acids Res,
36,
1805-1812.
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PDB code:
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J.A.Nelson,
and
O.C.Uhlenbeck
(2008).
Hammerhead redux: does the new structure fit the old biochemical data?
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RNA,
14,
605-615.
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M.Forconi,
J.Lee,
J.K.Lee,
J.A.Piccirilli,
and
D.Herschlag
(2008).
Functional identification of ligands for a catalytic metal ion in group I introns.
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Biochemistry,
47,
6883-6894.
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A.Matsugami,
Y.Xu,
Y.Noguchi,
H.Sugiyama,
and
M.Katahira
(2007).
Structure of a human telomeric DNA sequence stabilized by 8-bromoguanosine substitutions, as determined by NMR in a K+ solution.
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FEBS J,
274,
3545-3556.
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PDB code:
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M.Forconi,
J.A.Piccirilli,
and
D.Herschlag
(2007).
Modulation of individual steps in group I intron catalysis by a peripheral metal ion.
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RNA,
13,
1656-1667.
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J.T.Stivers,
and
R.Nagarajan
(2006).
Probing enzyme phosphoester interactions by combining mutagenesis and chemical modification of phosphate ester oxygens.
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Chem Rev,
106,
3443-3467.
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G.L.Olsen,
T.E.Edwards,
P.Deka,
G.Varani,
S.T.Sigurdsson,
and
G.P.Drobny
(2005).
Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR.
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Nucleic Acids Res,
33,
3447-3454.
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A.Lupták,
and
J.A.Doudna
(2004).
Distinct sites of phosphorothioate substitution interfere with folding and splicing of the Anabaena group I intron.
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Nucleic Acids Res,
32,
2272-2280.
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P.S.Klosterman,
D.K.Hendrix,
M.Tamura,
S.R.Holbrook,
and
S.E.Brenner
(2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
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Nucleic Acids Res,
32,
2342-2352.
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A.Matsugami,
S.Kobayashi,
K.Ouhashi,
S.Uesugi,
R.Yamamoto,
K.Taira,
S.Nishikawa,
P.K.Kumar,
and
M.Katahira
(2003).
Structural basis of the highly efficient trapping of the HIV Tat protein by an RNA aptamer.
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Structure,
11,
533-545.
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PDB code:
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A.Matsugami,
T.Okuizumi,
S.Uesugi,
and
M.Katahira
(2003).
Intramolecular higher order packing of parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad of GGA triplet repeat DNA.
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J Biol Chem,
278,
28147-28153.
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PDB code:
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N.J.Reiter,
L.J.Nikstad,
A.M.Allmann,
R.J.Johnson,
and
S.E.Butcher
(2003).
Structure of the U6 RNA intramolecular stem-loop harboring an S(P)-phosphorothioate modification.
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RNA,
9,
533-542.
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PDB codes:
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V.J.DeRose
(2003).
Metal ion binding to catalytic RNA molecules.
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Curr Opin Struct Biol,
13,
317-324.
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S.M.Crary,
J.C.Kurz,
and
C.A.Fierke
(2002).
Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P.
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RNA,
8,
933-947.
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T.C.Mou,
and
D.M.Gray
(2002).
The high binding affinity of phosphorothioate-modified oligomers for Ff gene 5 protein is moderated by the addition of C-5 propyne or 2'-O-methyl modifications.
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Nucleic Acids Res,
30,
749-758.
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D.Dertinger,
and
O.C.Uhlenbeck
(2001).
Evaluation of methylphosphonates as analogs for detecting phosphate contacts in RNA-protein complexes.
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RNA,
7,
622-631.
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H.Wu,
P.K.Yang,
S.E.Butcher,
S.Kang,
G.Chanfreau,
and
J.Feigon
(2001).
A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase III.
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EMBO J,
20,
7240-7249.
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PDB codes:
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J.L.O'Rear,
S.Wang,
A.L.Feig,
L.Beigelman,
O.C.Uhlenbeck,
and
D.Herschlag
(2001).
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.
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RNA,
7,
537-545.
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M.Lindqvist,
K.Sandström,
V.Liepins,
R.Strömberg,
and
A.Gräslund
(2001).
Specific metal-ion binding sites in a model of the P4-P6 triple-helical domain of a group I intron.
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RNA,
7,
1115-1125.
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T.C.Mou,
C.W.Gray,
T.C.Terwilliger,
and
D.M.Gray
(2001).
Ff gene 5 protein has a high binding affinity for single-stranded phosphorothioate DNA.
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Biochemistry,
40,
2267-2275.
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U.Stelzl,
and
K.H.Nierhaus
(2001).
A short fragment of 23S rRNA containing the binding sites for two ribosomal proteins, L24 and L4, is a key element for rRNA folding during early assembly.
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RNA,
7,
598-609.
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Y.Takagi,
M.Warashina,
W.J.Stec,
K.Yoshinari,
and
K.Taira
(2001).
Recent advances in the elucidation of the mechanisms of action of ribozymes.
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Nucleic Acids Res,
29,
1815-1834.
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D.Drygin,
and
R.A.Zimmermann
(2000).
Magnesium ions mediate contacts between phosphoryl oxygens at positions 2122 and 2176 of the 23S rRNA and ribosomal protein L1.
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RNA,
6,
1714-1726.
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M.Maderia,
L.M.Hunsicker,
and
V.J.DeRose
(2000).
Metal-phosphate interactions in the hammerhead ribozyme observed by 31P NMR and phosphorothioate substitutions.
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Biochemistry,
39,
12113-12120.
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T.E.Horton,
M.Maderia,
and
V.J.DeRose
(2000).
Impact of phosphorothioate substitutions on the thermodynamic stability of an RNA GAAA tetraloop: an unexpected stabilization.
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Biochemistry,
39,
8201-8207.
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Where a reference describes a PDB structure, the PDB
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