389d: Difference between revisions

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

OverviewOverview

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.

About this StructureAbout this Structure

Full crystallographic information is available from OCA.

ReferenceReference

Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability., Berger I, Tereshko V, Ikeda H, Marquez VE, Egli M, Nucleic Acids Res. 1998 May 15;26(10):2473-80. PMID:9580702 Page seeded by OCA on Sun May 4 20:18:29 2008

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OCA

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 [[Image:389d.gif|left|200px]]
- {{Structure
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-|SITE=
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-|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAF:2&#39;-DEOXY-2&#39;-FLUORO-ARABINO-FURANOSYL+THYMINE-5&#39;-PHOSPHATE'>TAF</scene>
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-|RELATEDENTRY=
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=389d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=389d OCA], [http://www.ebi.ac.uk/pdbsum/389d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=389d RCSB]</span>
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 '''CRYSTAL STRUCTURE OF B-DNA WITH INCORPORATED 2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINES: IMPLICATIONS OF CONFORMATIONAL PREORGANIZATION FOR DUPLEX STABILITY'''
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 ==About this Structure==
-D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=389D OCA].
+Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=389D OCA].
 ==Reference==
 Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability., Berger I, Tereshko V, Ikeda H, Marquez VE, Egli M, Nucleic Acids Res. 1998 May 15;26(10):2473-80. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9580702 9580702]
-[[Category: Protein complex]]
 [[Category: Berger, I.]]
 [[Category: Egli, M.]]
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 [[Category: Marquez, V E.]]
 [[Category: Tereshko, V.]]
-[[Category: b-dna]]
+[[Category: B-dna]]
-[[Category: double helix]]
+[[Category: Double helix]]
-[[Category: modified]]
+[[Category: Modified]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:18:29 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:22:03 2008''