Impact of the 8-oxoguanine on B-DNA molecule; Molecular dynamics study

Pinak, M.

The local structural and energetic impact of a mutagenic oxidative lesion 7,8-dihydro-8-oxoguanine (8-oxoG) on a DNA molecule was studied by the method of a molecular dynamics (MD) simulation. The molecule of 8-oxoG was inserted into central part of B-DNA 15-mer d(GCGTCCA'8-oxoG'GTCTACC) replacing the native guanine. The 2-nanosecond MD simulations were performed with the AMBER 5.0 program code at the constant temperature of 310 K (36.5ºC, temperature of human body) for the 8-oxoG lesioned and native DNA molecules. The broken hydrogen bonds resulting in locally collapsed B-DNA structure were observed at the lesion site. The adenine 21 on the complementary strand (separated from 8-oxoG by 1 base pair) is flipped-out of the DNA double helix. Its extrahelical position forms a hole that may favor docking of repair enzyme into DNA during repair process. A strong electrostatic repulsion between nucleotide with the 8-oxoG and neighboring nucleotides contributes to the observed instability of DNA at the lesion.