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PDBsum entry 1d9f
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Transferase/DNA, RNA
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PDB id
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1d9f
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural origins of the exonuclease resistance of a zwitterionic RNA.
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Authors
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M.Teplova,
S.T.Wallace,
V.Tereshko,
G.Minasov,
A.M.Symons,
P.D.Cook,
M.Manoharan,
M.Egli.
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Ref.
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Proc Natl Acad Sci U S A, 1999,
96,
14240-14245.
[DOI no: ]
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PubMed id
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Abstract
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Nuclease resistance and RNA affinity are key criteria in the search for optimal
antisense nucleic acid modifications, but the origins of the various levels of
resistance to nuclease degradation conferred by chemical modification of DNA and
RNA are currently not understood. The 2'-O-aminopropyl (AP)-RNA modification
displays the highest nuclease resistance among all phosphodiester-based
analogues and its RNA binding affinity surpasses that of phosphorothioate DNA by
1 degrees C per modified residue. We found that oligodeoxynucleotides containing
AP-RNA residues at their 3' ends competitively inhibit the degradation of
single-stranded DNA by the Escherichia coli Klenow fragment (KF) 3'-5'
exonuclease and snake venom phosphodiesterase. To shed light on the origins of
nuclease resistance brought about by the AP modification, we determined the
crystal structure of an A-form DNA duplex with AP-RNA modifications at 1.6-A
resolution. In addition, the crystal structures of complexes between short DNA
fragments carrying AP-RNA modifications and wild-type KF were determined at
resolutions between 2.2 and 3.0 A and compared with the structure of the complex
between oligo(dT) and the D355A/E357A KF mutant. The structural models suggest
that interference of the positively charged 2'-O-substituent with the metal ion
binding site B of the exonuclease allows AP-RNA to effectively slow down
degradation.
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Figure 1.
Fig. 1. Chemical structures of DNA, PS-DNA, AP-RNA, and
2'-O-butyl RNA.
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Figure 7.
Fig. 7. The two orientations and resulting interactions
of d(T)-AP(U)-d(T)-3' at the wt-KF exonuclease active site. Only
one of the orientations is compatible with a direct
phosphate-metal ion interaction (A). However, the Zn2+ ... 0
distance is longer (2.49 Å) compared with the hexamer
complex (1.81 Å, Fig. 6A). See Fig. 6 for color scheme and
further explanations.
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