1puy
From Proteopedia
(New page: 200px<br /><applet load="1puy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1puy, resolution 1.50Å" /> '''1.5 A resolution str...) |
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| - | [[Image:1puy.gif|left|200px]]<br /><applet load="1puy" size=" | + | [[Image:1puy.gif|left|200px]]<br /><applet load="1puy" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1puy, resolution 1.50Å" /> | caption="1puy, resolution 1.50Å" /> | ||
'''1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker'''<br /> | '''1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Synthetic conjugates possessing bis(2-hydroxyethyl)stilbene-4,4'-diether | + | Synthetic conjugates possessing bis(2-hydroxyethyl)stilbene-4,4'-diether linkers (Sd2) form the most stable DNA hairpins reported to date. Factors that affect stability are length and flexibility of the linkers and pi-stacking of the stilbene moiety on the adjacent base pair. The crystal structure of the hairpin d(GT(4)G)-Sd2-d(CA(4)C) was determined at 1.5 A resolution. The conformations of the two molecules in the asymmetric unit differ both in the linker and the stem portions. One of them shows a planar stilbene that is stacked on the adjacent G:C base pair. The other displays considerable rotation between the phenyl rings and an unprecedented edge-to-face orientation of stilbene and base pair. The observation of considerable variations in the conformation of the Sd moiety in the crystal structure allows us to exclude restriction of motion as the reason for the absence of Sd photoisomerization in the hairpins. Conformational differences in the stem portion of the two hairpin molecules go along with different Mg(2+) binding modes. Most remarkable among them is the sequence-specific coordination of a metal ion in the narrow A-tract minor groove. The crystal structure provides unequivocal evidence that a fully hydrated Mg(2+) ion can penetrate the narrow A-tract minor groove, causing the groove to further contract. Overall, the structural data provide a better understanding of the origins of hairpin stability and their photochemical behavior in solution. |
==About this Structure== | ==About this Structure== | ||
| - | 1PUY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1PUY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PUY OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Egli, M.]] | [[Category: Egli, M.]] | ||
| - | [[Category: Lewis, F | + | [[Category: Lewis, F D.]] |
[[Category: Liu, X.]] | [[Category: Liu, X.]] | ||
[[Category: Murshudov, G.]] | [[Category: Murshudov, G.]] | ||
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[[Category: dna]] | [[Category: dna]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:32:52 2008'' |
Revision as of 12:32, 21 February 2008
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1.5 A resolution structure of a synthetic DNA hairpin with a stilbenediether linker
Overview
Synthetic conjugates possessing bis(2-hydroxyethyl)stilbene-4,4'-diether linkers (Sd2) form the most stable DNA hairpins reported to date. Factors that affect stability are length and flexibility of the linkers and pi-stacking of the stilbene moiety on the adjacent base pair. The crystal structure of the hairpin d(GT(4)G)-Sd2-d(CA(4)C) was determined at 1.5 A resolution. The conformations of the two molecules in the asymmetric unit differ both in the linker and the stem portions. One of them shows a planar stilbene that is stacked on the adjacent G:C base pair. The other displays considerable rotation between the phenyl rings and an unprecedented edge-to-face orientation of stilbene and base pair. The observation of considerable variations in the conformation of the Sd moiety in the crystal structure allows us to exclude restriction of motion as the reason for the absence of Sd photoisomerization in the hairpins. Conformational differences in the stem portion of the two hairpin molecules go along with different Mg(2+) binding modes. Most remarkable among them is the sequence-specific coordination of a metal ion in the narrow A-tract minor groove. The crystal structure provides unequivocal evidence that a fully hydrated Mg(2+) ion can penetrate the narrow A-tract minor groove, causing the groove to further contract. Overall, the structural data provide a better understanding of the origins of hairpin stability and their photochemical behavior in solution.
About this Structure
1PUY is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Face-to-face and edge-to-face pi-pi interactions in a synthetic DNA hairpin with a stilbenediether linker., Egli M, Tereshko V, Mushudov GN, Sanishvili R, Liu X, Lewis FD, J Am Chem Soc. 2003 Sep 10;125(36):10842-9. PMID:12952463
Page seeded by OCA on Thu Feb 21 14:32:52 2008
Categories: Protein complex | Egli, M. | Lewis, F D. | Liu, X. | Murshudov, G. | Sanishvili, R. | Tereshko, V. | MG | Dna
