1d9h

From Proteopedia

Revision as of 09:12, 23 January 2008

Structural origins of the exonuclease resistance of a zwitterionic RNA

Overview

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.

About this Structure

1D9H is a Single protein structure of sequence from [1]. Full crystallographic information is available from OCA.

Reference

Structural origins of the exonuclease resistance of a zwitterionic RNA., Teplova M, Wallace ST, Tereshko V, Minasov G, Symons AM, Cook PD, Manoharan M, Egli M, Proc Natl Acad Sci U S A. 1999 Dec 7;96(25):14240-5. PMID:10588690

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