Solution Structure of an Oligodeoxynucleotide Containing the Malondialdehyde Deoxyguanosine Adduct N2-(3-Oxo-1-propenyl)-dG (Ring-Opened M1G) Positioned in a (CpG)3 Frameshift Hotspot of the Salmonella typhimurium hisD3052 Gene
- 24 September 1999
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 38 (41) , 13491-13501
- https://doi.org/10.1021/bi9910124
Abstract
The refined solution structure for the ring-opened N2-(3-oxo-1-propenyl)-dG derivative of the malondialdehyde deoxyguanosine adduct M1G [3-(2‘-deoxy-β-d-erythro-pentofuranosyl)pyrimido[1,2-a]purin-10(3H)-one] in d(ATCGCXCGGCATG)·d(CATGCCGCGCGAT) [X being N2-(3-oxo-1-propenyl)-dG], containing the d(CpG)3 frameshift hotspot of the Salmonella typhimuriumhisD3052 gene, is presented. When inserted into this duplex, M1G underwent spontaneous ring opening to N2-(3-oxo-1-propenyl)-dG. NMR analysis revealed that N2-(3-oxo-1-propenyl)-dG induced minor structural perturbations in the hisD3052 oligodeoxynucleotide. However, the stability of the duplex DNA was reduced; the N2-(3-oxo-1-propenyl)-dG-modified hisD3052 oligodeoxynucleotide exhibited a 14 °C decrease in Tm relative to that of the native oligodeoxynucleotide. The modified guanine maintained stacking interactions with neighboring bases but was not Watson−Crick hydrogen bonded. A total of 13 NOEs were observed from the 3-oxo-1-propenyl moiety protons of N2-(3-oxo-1-propenyl)-dG to DNA protons. Molecular dynamics calculations, restrained by 602 distance restraints derived from experimental NOE measurements and 23 empirical distance restraints, converged with pairwise rmsd differences of -2. The cytosine complementary to N2-(3-oxo-1-propenyl)-dG was pushed toward the major groove but maintained partial stacking interactions with its neighboring bases. The modified guanine remained in the anti conformation, while the 3-oxo-1-propenyl moiety was positioned in the minor groove of the duplex. Possible correlations between the relatively small structural perturbations induced in this DNA duplex by N2-(3-oxo-1-propenyl)-dG and the mutagenic spectrum of M1G are discussed.Keywords
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