1luh
From Proteopedia
(New page: 200px<br /><applet load="1luh" size="450" color="white" frame="true" align="right" spinBox="true" caption="1luh" /> '''SOLUTION NMR STRUCTURE OF SELF-COMPLIMENTARY...) |
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| - | [[Image:1luh.jpg|left|200px]]<br /><applet load="1luh" size=" | + | [[Image:1luh.jpg|left|200px]]<br /><applet load="1luh" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1luh" /> | caption="1luh" /> | ||
'''SOLUTION NMR STRUCTURE OF SELF-COMPLIMENTARY DUPLEX 5'-D(TCCG*CGGA)2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*'''<br /> | '''SOLUTION NMR STRUCTURE OF SELF-COMPLIMENTARY DUPLEX 5'-D(TCCG*CGGA)2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Malondialdehyde interstrand cross-links in DNA show strong preference for | + | Malondialdehyde interstrand cross-links in DNA show strong preference for 5'-d(CpG) sequences. The cross-links are unstable and a trimethylene cross-link has been used as a surrogate for structural studies. A previous structural study of the 5'-d(CpG) cross-link in the sequence 5'-d(AGGCGCCT), where G is the modified nucleotide, by NMR spectroscopy and molecular dynamics using a simulated annealing protocol showed the guanine residues and the tether lay approximately in a plane such that the trimethylene tether and probably the malondialdehyde tether, as well, could be accommodated without major disruptions of duplex structure [Dooley et al. J. Am Chem. Soc. 2001, 123, 1730-1739]. The trimethylene cross-link has now been studied in a GpC motif using the reverse sequence. The structure lacks the planarity seen with the 5'-d(CpG) sequence and is skewed about the trimethylene cross-link. Melting studies indicate that the trimethylene cross-link is thermodynamically less stable in the GpC motif than in the 5-d(CpG). Furthermore, lack of planarity of the GpC cross-link precludes making an isosteric replacement of the trimethylene tether by malondialdehyde. A similar argument can be used to explain the 5'-d(CpG) preference for interchain cross-linking by acrolein. |
==About this Structure== | ==About this Structure== | ||
| - | 1LUH is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with TME as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1LUH is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=TME:'>TME</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LUH OCA]. |
==Reference== | ==Reference== | ||
NMR determination of the conformation of a trimethylene interstrand cross-link in an oligodeoxynucleotide duplex containing a 5'-d(GpC) motif., Dooley PA, Zhang M, Korbel GA, Nechev LV, Harris CM, Stone MP, Harris TM, J Am Chem Soc. 2003 Jan 8;125(1):62-72. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12515507 12515507] | NMR determination of the conformation of a trimethylene interstrand cross-link in an oligodeoxynucleotide duplex containing a 5'-d(GpC) motif., Dooley PA, Zhang M, Korbel GA, Nechev LV, Harris CM, Stone MP, Harris TM, J Am Chem Soc. 2003 Jan 8;125(1):62-72. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12515507 12515507] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Dooley, P | + | [[Category: Dooley, P D.]] |
| - | [[Category: Harris, C | + | [[Category: Harris, C M.]] |
| - | [[Category: Harris, T | + | [[Category: Harris, T M.]] |
| - | [[Category: Korbel, G | + | [[Category: Korbel, G A.]] |
| - | [[Category: Nechev, L | + | [[Category: Nechev, L V.]] |
| - | [[Category: Stone, M | + | [[Category: Stone, M P.]] |
[[Category: Zhang, M.]] | [[Category: Zhang, M.]] | ||
[[Category: TME]] | [[Category: TME]] | ||
| Line 23: | Line 23: | ||
[[Category: guanine n2-guanine n2 interstrand crosslink]] | [[Category: guanine n2-guanine n2 interstrand crosslink]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:48:37 2008'' |
Revision as of 11:48, 21 February 2008
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SOLUTION NMR STRUCTURE OF SELF-COMPLIMENTARY DUPLEX 5'-D(TCCG*CGGA)2 CONTAINING A TRIMETHYLENE CROSSLINK AT THE N2 POSITION OF G*
Overview
Malondialdehyde interstrand cross-links in DNA show strong preference for 5'-d(CpG) sequences. The cross-links are unstable and a trimethylene cross-link has been used as a surrogate for structural studies. A previous structural study of the 5'-d(CpG) cross-link in the sequence 5'-d(AGGCGCCT), where G is the modified nucleotide, by NMR spectroscopy and molecular dynamics using a simulated annealing protocol showed the guanine residues and the tether lay approximately in a plane such that the trimethylene tether and probably the malondialdehyde tether, as well, could be accommodated without major disruptions of duplex structure [Dooley et al. J. Am Chem. Soc. 2001, 123, 1730-1739]. The trimethylene cross-link has now been studied in a GpC motif using the reverse sequence. The structure lacks the planarity seen with the 5'-d(CpG) sequence and is skewed about the trimethylene cross-link. Melting studies indicate that the trimethylene cross-link is thermodynamically less stable in the GpC motif than in the 5-d(CpG). Furthermore, lack of planarity of the GpC cross-link precludes making an isosteric replacement of the trimethylene tether by malondialdehyde. A similar argument can be used to explain the 5'-d(CpG) preference for interchain cross-linking by acrolein.
About this Structure
1LUH is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
NMR determination of the conformation of a trimethylene interstrand cross-link in an oligodeoxynucleotide duplex containing a 5'-d(GpC) motif., Dooley PA, Zhang M, Korbel GA, Nechev LV, Harris CM, Stone MP, Harris TM, J Am Chem Soc. 2003 Jan 8;125(1):62-72. PMID:12515507
Page seeded by OCA on Thu Feb 21 13:48:37 2008
