1luh
From Proteopedia
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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 TME 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
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