title: Structural studies of an oligodeoxynucleotide containing a trimethylene interstrand cross-link in a 5'-(CpG) motif: model of a malondialdehyde cross-link.
abstract: Malondialdehyde (MDA), a known mutagen and suspected carcinogen, is a product of lipid peroxidation and byproduct of eicosanoid biosynthesis. MDA can react with DNA to generate potentially mutagenic adducts on adenine, cytosine, and particularly guanine. In addition, repair-dependent frame shift mutations in a GCGCGC region of Salmonella typhimurium hisD3052 have been attributed to formation of interstrand cross-links (Mukai, F. H. and Goldstein, B. D. Science 1976, 191, 868--869). The cross-linked species is unstable and has never been characterized but has been postulated to be a bis-imino linkage between N(2) positions of guanines. An analogous linkage has now been investigated as a stable surrogate using the self-complementary oligodeoxynucleotide sequence 5'-d(AGGCG*CCT)(2,) in which G* represents guanines linked via a trimethylene chain between N(2) positions. The solution structure, obtained by NMR spectroscopy and molecular dynamics using a simulated annealing protocol, revealed the cross-link only minimally distorts duplex structure in the region of the cross-link. The tether is accommodated by partially unwinding the duplex at the lesion site to produce a bulge and tipping the guanine residues; the two guanines and the tether attain a nearly planar conformation. This distortion did not result in significant bending of the DNA, a result which was confirmed by gel electrophoresis studies of multimers of a 21-mer duplex containing the cross-link.
authors.affiliation: Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA.
authors.forename: P A
authors.initials: PA
authors.lastname: Dooley
authors.forename: D
authors.initials: D
authors.lastname: Tsarouhtsis
authors.forename: G A
authors.initials: GA
authors.lastname: Korbel
authors.forename: L V
authors.initials: LV
authors.lastname: Nechev
authors.forename: J
authors.initials: J
authors.lastname: Shearer
authors.forename: I S
authors.initials: IS
authors.lastname: Zegar
authors.forename: C M
authors.initials: CM
authors.lastname: Harris
authors.forename: M P
authors.initials: MP
authors.lastname: Stone
authors.forename: T M
authors.initials: TM
authors.lastname: Harris
mesh_terms: D001483:Base Sequence; D003432:Cross-Linking Reagents / Q000737:chemistry*; D003521:Cyclopropanes / Q000737:chemistry*; D015777:Eicosanoids / Q000096:biosynthesis / Q000737:chemistry; D006147:Guanine / Q000737:chemistry*; D015227:Lipid Peroxidation / Q000502:physiology; D009682:Magnetic Resonance Spectroscopy; D008315:Malondialdehyde / Q000737:chemistry*; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*
chemical_list: D003432:Cross-Linking Reagents; D003521:Cyclopropanes; D015777:Eicosanoids; D009841:Oligonucleotides; D008315:Malondialdehyde; D006147:Guanine; C030797:cyclopropane