Structural studies of an oligodeoxynucleotide containing a trimethylene interstrand cross-link in a 5 '-(CpG) motif: Model of a malondialdehyde cross-link

Malondialdehyde (MDA), a known mutagen and suspected carcinogen, is a produ ct of lipid peroxidation and byproduct of eicosanoid biosynthesis. MDA can react with DNA to generate potentially mutagenic adducts on adenine, cytosi ne, and particularly guanine. In addition, repair-dependent frame shift mut ations in a GCGCGC region of Salmonella typhimurium hisD3052 have been attr ibuted to formation of interstrand cross-links (Mukai, F. H. and Goldstein, B. D. Science 1976, 191, 868-869). The cross-linked species is unstable an d has never been characterized but has been postulated to be a bis-imino li nkage between N-2 positions of guanines. An analogous linkage has now been investigated as a stable surrogate using the self-complementary oligodeoxyn ucleotide sequence 5'-d(AGGCG*CCT)(2), in which G* represents guanines link ed via a trimethylene chain between NZ positions. The solution structure, o btained by NMR spectroscopy and molecular dynamics using a simulated anneal ing protocol, revealed the cross-link only minimally distorts duplex struct ure in the region of the cross-link. The tether is accommodated by partiall y unwinding the duplex at the lesion site to produce a bulge and tipping th e guanine residues; the two guanines and the tether attain at the lesion si te to produce a bulge and tipping the guanine resideues; the two guanines a nd the tether attain a nearly planar conformation. This distortion did not result in significant bending of the DNA, a result which was confirmed by g el electrophoresis studies of multimers of a 21-mer duplex containing the c ross-link.