Modeling of mechanochemical DNA cleavage by action of ultrasound
Nechupurenko, D.I.; Il'icheva, I.A.; Khodykov, M.V.; Poptsova, M.S.; Nechipurenko, I.D.; Grokhovskiĭ, S.L.
Biofizika 59(6): 1061-1070
2014
ISSN/ISBN: 0006-3029 PMID: 25715610 Document Number: 678329
This study offers a simulation of the stretching dynamics of a double-stranded DNA fragment in the high-gradient flow of fluid near collapsing cavitation bubbles. Calculated profiles of elastic tension along the model of a polymer fragment were used to estimate the rates of mechanochemical cleavage at different positions of DNA restriction fragments. The resulting cleavage rate profiles are qualitatively consistent with the experimentally observed profiles of ultrasonic cleavage rates of DNA restriction fragments, which are position-dependent. The proposed model also relates the sequence specificity of ultrasonic DNA cleavage, which was experimentally detected earlier, to the peculiarities of sequence-specific conformational dynamics of β-D-deoxyribose in the B-form double helix. A quantitative assessment of the ultrasonic DNA cleavage rates for different conformational states of β-D-deoxyribose derived from the proposed model qualitatively agrees with the experimental data.