1icg
From Proteopedia
(New page: 200px<br /><applet load="1icg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1icg, resolution 1.53Å" /> '''STRUCTURE OF THE HYB...) |
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| - | [[Image:1icg.gif|left|200px]]<br /><applet load="1icg" size=" | + | [[Image:1icg.gif|left|200px]]<br /><applet load="1icg" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1icg, resolution 1.53Å" /> | caption="1icg, resolution 1.53Å" /> | ||
'''STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF IR(NH3)6+++'''<br /> | '''STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF IR(NH3)6+++'''<br /> | ||
==Overview== | ==Overview== | ||
| - | In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA | + | In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions. |
==About this Structure== | ==About this Structure== | ||
| - | 1ICG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with CL and IRI as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http:// | + | 1ICG is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CL:'>CL</scene> and <scene name='pdbligand=IRI:'>IRI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ICG OCA]. |
==Reference== | ==Reference== | ||
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[[Category: rna/dna hybrid]] | [[Category: rna/dna hybrid]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:10:23 2008'' |
Revision as of 11:10, 21 February 2008
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STRUCTURE OF THE HYBRID RNA/DNA R-GCUUCGGC-D[F]U IN PRESENCE OF IR(NH3)6+++
Overview
In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions.
About this Structure
1ICG is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues., Cruse W, Saludjian P, Neuman A, Prange T, Acta Crystallogr D Biol Crystallogr. 2001 Nov;57(Pt 11):1609-13. Epub 2001, Oct 25. PMID:11679725
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