389D

CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY

Summary for 389D

• Entry DOI: 10.2210/pdb389d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*GP*CP*G)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: b-dna, double helix, modified, dna
• Total number of polymer chains: 2
• Total formula weight: 7387.07

Authors

Berger, I.,Tereshko, V.,Ikeda, H.,Marquez, V.E.,Egli, M. (deposition date: 1998-04-20, release date: 1998-05-05, Last modification date: 2024-02-21)

Primary citation

Berger, I.,Tereshko, V.,Ikeda, H.,Marquez, V.E.,Egli, M.
Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability.
Nucleic Acids Res., 26:2473-2480, 1998

PubMed Abstract: The fundamental conformational states of right-handed double helical DNA, the A- and B-forms, are associated with distinct puckers of the sugar moieties. The furanose conformation itself is affected by the steric and electronic nature of the ring substituents. For example, a strongly electronegative substituent at the C2' position, such as in the 2'-deoxy-2'-fluoro ribo furanosyl analogue, will drive the conformational equilibrium towards the C3'- endo type (north). Conversely, the 2'-deoxy-2'-fluoro arabino furanosyl modification with opposite stereochemistry at C2' appears to have a preference for a C2'- endo type pucker (south). Incorporation of 2'-fluoroarabinofuranosyl thymines was previously shown to enhance the thermodynamic stability of B-DNA duplexes. We have determined the crystal structures of the B-DNA dodecamer duplexes [d(CGCGAASSCGCG)]2and [d(CGCGAASTCGCG)]2with incorporated 2'-deoxy-2'-fluoroarabinofuranosyl thymines S (south) at 1.55 A resolution. In the crystal structures, all S residues adopt an O4'- endo conformation (east), well compatible with an overall B-form duplex geometry. In addition to the increased rigidity of S nucleosides, a clathrate-like ordered water structure around the 2'-fluorines may account for the observed larger thermodynamic stability of DNA duplexes containing 2'-deoxy-2'-fluoroarabino thymidines.

PubMed: 9580702
DOI: 10.1093/nar/26.10.2473

Experimental method

X-RAY DIFFRACTION (1.55 Å)