233d: Difference between revisions

Revision as of 17:21, 21 February 2008

THE CRYSTAL STRUCTURE ANALYSIS OF D(CGCGAASSCGCG)2: A SYNTHETIC DNA DODECAMER DUPLEX CONTAINING FOUR 4'-THIO-2'-DEOXYTHYMIDINE NUCLEOTIDES

OverviewOverview

The crystal structure refinement of the synthetic dodecamer d(CGCGAASSCGCG), where S = 4'-thio-2'-deoxythymidine, has converged at R=0.201 for 2605 reflections with F > 2sigma(F) in the resolution range 8.0-2.4 A for a model consisting of the dodecamer duplex and 66 water molecules. A comparison of its structure with that of the native dodecamer d(CGCGAATTCGCG) has revealed that the major differences between the two structures is a change in the conformation of the sugar-phosphate backbone in the regions at and adjacent to the positions of the modified nucleosides. Examination of the fine structural parameters for each of the structures reveals that the thiosugars adopt a C3'-exo conformation in d(CGCGAASSCGCG), rather than the approximate C1'-exo conformation found for the analogous sugars in the structure of d(CGCGAATTCGCG). The observed differences in structure between the two duplexes may help to explain the enhanced resistance to nuclease digestion of synthetic oligonucleotides containing 4'-thio-2'-deoxynucleotides.

About this StructureAbout this Structure

233D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

ReferenceReference

The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides., Boggon TJ, Hancox EL, McAuley-Hecht KE, Connolly BA, Hunter WN, Brown T, Walker RT, Leonard GA, Nucleic Acids Res. 1996 Mar 1;24(5):951-61. PMID:8600465

Page seeded by OCA on Thu Feb 21 16:21:23 2008

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OCA

@@ Line 4: / Line 4: @@
 ==Overview==
-The crystal structure refinement of the synthetic dodecamer, d(CGCGAASSCGCG), where S = 4'-thio-2'-deoxythymidine, has converged at, R=0.201 for 2605 reflections with F &gt; 2sigma(F) in the resolution range, 8.0-2.4 A for a model consisting of the dodecamer duplex and 66 water, molecules. A comparison of its structure with that of the native dodecamer, d(CGCGAATTCGCG) has revealed that the major differences between the two, structures is a change in the conformation of the sugar-phosphate backbone, in the regions at and adjacent to the positions of the modified, nucleosides. Examination of the fine structural parameters for each of the, structures reveals that the thiosugars adopt a C3'-exo conformation in, d(CGCGAASSCGCG), rather than the approximate C1'-exo conformation found, for the analogous sugars in the structure of d(CGCGAATTCGCG). The observed, differences in structure between the two duplexes may help to explain the, enhanced resistance to nuclease digestion of synthetic oligonucleotides, containing 4'-thio-2'-deoxynucleotides.
+The crystal structure refinement of the synthetic dodecamer d(CGCGAASSCGCG), where S = 4'-thio-2'-deoxythymidine, has converged at R=0.201 for 2605 reflections with F &gt; 2sigma(F) in the resolution range 8.0-2.4 A for a model consisting of the dodecamer duplex and 66 water molecules. A comparison of its structure with that of the native dodecamer d(CGCGAATTCGCG) has revealed that the major differences between the two structures is a change in the conformation of the sugar-phosphate backbone in the regions at and adjacent to the positions of the modified nucleosides. Examination of the fine structural parameters for each of the structures reveals that the thiosugars adopt a C3'-exo conformation in d(CGCGAASSCGCG), rather than the approximate C1'-exo conformation found for the analogous sugars in the structure of d(CGCGAATTCGCG). The observed differences in structure between the two duplexes may help to explain the enhanced resistance to nuclease digestion of synthetic oligonucleotides containing 4'-thio-2'-deoxynucleotides.
 ==About this Structure==
@@ Line 12: / Line 12: @@
 The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides., Boggon TJ, Hancox EL, McAuley-Hecht KE, Connolly BA, Hunter WN, Brown T, Walker RT, Leonard GA, Nucleic Acids Res. 1996 Mar 1;24(5):951-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8600465 8600465]
 [[Category: Protein complex]]
-[[Category: Boggon, T.J.]]
+[[Category: Boggon, T J.]]
 [[Category: Brown, T.]]
-[[Category: Connolly, B.A.]]
+[[Category: Connolly, B A.]]
-[[Category: Hancox, E.L.]]
+[[Category: Hancox, E L.]]
-[[Category: Hunter, W.N.]]
+[[Category: Hunter, W N.]]
-[[Category: Leonard, G.A.]]
+[[Category: Leonard, G A.]]
-[[Category: McAuley-Hecht, K.E.]]
+[[Category: McAuley-Hecht, K E.]]
-[[Category: Walker, R.T.]]
+[[Category: Walker, R T.]]
 [[Category: b-dna]]
 [[Category: double helix]]
 [[Category: modified]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:48:18 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:21:23 2008''