DSSR-PyMOL cartoon-block schematics: PDB entry 233d

PDB-id

233d; DSSR-derived features in text and JSON formats

Class

DNA

Method

X-ray (2.4 Å)

Summary

The crystal structure analysis of d(cgcgaasscgcg)2: a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides

Reference

Boggon TJ, Hancox EL, McAuley-Hecht KE, Connolly BA, Hunter WN, Brown T, Walker RT, Leonard GA (1996): "The crystal structure analysis of d(CGCGAASSCGCG)2, a synthetic DNA dodecamer duplex containing four 4'-thio-2'-deoxythymidine nucleotides." Nucleic Acids Res., 24, 951-961. doi: 10.1093/nar/24.5.951.

Abstract

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.