1oo7
From Proteopedia
(New page: 200px<br /><applet load="1oo7" size="450" color="white" frame="true" align="right" spinBox="true" caption="1oo7" /> '''DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE...) |
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| - | [[Image:1oo7.gif|left|200px]]<br /><applet load="1oo7" size=" | + | [[Image:1oo7.gif|left|200px]]<br /><applet load="1oo7" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1oo7" /> | caption="1oo7" /> | ||
'''DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES'''<br /> | '''DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The addition of the propynyl group at the 5 position of pyrimidine | + | The addition of the propynyl group at the 5 position of pyrimidine nucleotides is highly stabilising. We have determined the thermodynamic stability of the DNA.RNA hybrid r(GAAGAGAAGC)*d(GC(p)U(p)U(p)C(p)U(p) C(p)U(p)U(p)C) where p is the propynyl group at the 5 position and compared it with that of the unmodified duplex and the effects of methyl substitutions. The incorporation of the propyne group at the 5 position gives rise to a very large stabilisation of the hybrid duplex compared with the analogous 5-Me modification. The duplexes have been characterised by gel electrophoresis and NMR spectroscopy, which indicate that methyl substitutions have a smaller influence on local and global conformation than the propynyl groups. The increased NMR spectral dispersion of the propyne-modified duplex allowed a larger number of experimental restraints to be measured. Restrained molecular dynamics in a fully solvated system showed that the propyne modification leads to substantial conformational rearrangements stabilising a more A-like structure. The propynyl groups occupy a large part of the major groove and make favourable van der Waals interactions with their nearest neighbours and the atoms of the rings. This enhanced overlap may account at least in part for the increased thermodynamic stability. Furthermore, the simulations show a spine of hydration in the major groove as well as in the minor groove involving the RNA hydroxyl groups. |
==About this Structure== | ==About this Structure== | ||
| - | 1OO7 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1OO7 is a [http://en.wikipedia.org/wiki/Protein_complex 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=1OO7 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Brown, T.]] | [[Category: Brown, T.]] | ||
| - | [[Category: Conn, G | + | [[Category: Conn, G L.]] |
[[Category: Gao, D.]] | [[Category: Gao, D.]] | ||
| - | [[Category: Gyi, J | + | [[Category: Gyi, J I.]] |
| - | [[Category: Lane, A | + | [[Category: Lane, A N.]] |
| - | [[Category: Trent, J | + | [[Category: Trent, J O.]] |
[[Category: antisense]] | [[Category: antisense]] | ||
| - | [[Category: dna | + | [[Category: dna rna hybrid]] |
[[Category: purine/pyrimidine-rich strands]] | [[Category: purine/pyrimidine-rich strands]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:19:51 2008'' |
Revision as of 12:19, 21 February 2008
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DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES
Overview
The addition of the propynyl group at the 5 position of pyrimidine nucleotides is highly stabilising. We have determined the thermodynamic stability of the DNA.RNA hybrid r(GAAGAGAAGC)*d(GC(p)U(p)U(p)C(p)U(p) C(p)U(p)U(p)C) where p is the propynyl group at the 5 position and compared it with that of the unmodified duplex and the effects of methyl substitutions. The incorporation of the propyne group at the 5 position gives rise to a very large stabilisation of the hybrid duplex compared with the analogous 5-Me modification. The duplexes have been characterised by gel electrophoresis and NMR spectroscopy, which indicate that methyl substitutions have a smaller influence on local and global conformation than the propynyl groups. The increased NMR spectral dispersion of the propyne-modified duplex allowed a larger number of experimental restraints to be measured. Restrained molecular dynamics in a fully solvated system showed that the propyne modification leads to substantial conformational rearrangements stabilising a more A-like structure. The propynyl groups occupy a large part of the major groove and make favourable van der Waals interactions with their nearest neighbours and the atoms of the rings. This enhanced overlap may account at least in part for the increased thermodynamic stability. Furthermore, the simulations show a spine of hydration in the major groove as well as in the minor groove involving the RNA hydroxyl groups.
About this Structure
1OO7 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
The solution structure of a DNA*RNA duplex containing 5-propynyl U and C; comparison with 5-Me modifications., Gyi JI, Gao D, Conn GL, Trent JO, Brown T, Lane AN, Nucleic Acids Res. 2003 May 15;31(10):2683-93. PMID:12736318
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