1d8y: Difference between revisions

Revision as of 13:14, 21 February 2008

CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA

OverviewOverview

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 StructureAbout this Structure

1D8Y is a Single protein structure of sequence from Escherichia coli with and as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Feb 21 12:14:15 2008

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OCA

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-[[Image:1d8y.gif|left|200px]]<br /><applet load="1d8y" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1d8y.gif|left|200px]]<br /><applet load="1d8y" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1d8y, resolution 2.08&Aring;" />
 '''CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA'''<br />
 ==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.
+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==
-D8Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with ZN and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D8Y OCA].
+D8Y is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D8Y OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Escherichia coli]]
 [[Category: Single protein]]
-[[Category: Cook, P.D.]]
+[[Category: Cook, P D.]]
 [[Category: Egli, M.]]
 [[Category: Manoharan, M.]]
 [[Category: Minasov, G.]]
-[[Category: Simons, A.M.]]
+[[Category: Simons, A M.]]
 [[Category: Teplova, M.]]
 [[Category: Tereshko, V.]]
-[[Category: Wallace, S.T.]]
+[[Category: Wallace, S T.]]
 [[Category: SO4]]
 [[Category: ZN]]
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 [[Category: poly-d(t)]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:05:30 2007''
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