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Mechanochemical Cleavage of DNA by Ultrasound (pp. 1-24) $100.00
Authors:  (Sergei L. Grokhovsky, Irina A. Il’icheva, Dmitry Yu. Nechipurenko, Mikhail V. Golovkin, Larisa A. Panchenko, Robert V. Polozov, Yury D. Nechipurenko, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, and others)
Abstract:
Ultrasonic cleavage of polymers has been a subject of intensive studies during the
past decades. Currently used experimental protocols and techniques of nucleic acids
manipulation allow us to conduct ultrasonic cleavage experiments with DNA fragments
of known length and base pair sequence. Further analysis of ultrasonic cleavage products
with polyacrylamide gel electrophoresis makes it possible to determine the exact
positions of DNA cleavage sites and corresponding cleavage efficiencies. In our study we
analyze the phenomenon of ultrasonic cleavage of DNA in details. Two main effects are
observed in DNA cleavage patterns: attenuation of ultrasonic cleavage at sites close to
the ends of the DNA fragments and sequence-specificity of cleavage. Here we propose
the model which accounts for these two effects. Our model describes the extension of the
DNA molecules in cavitational flow that leads to the mechanochemical cleavage of
DNA. The sequence specificity of ultrasonic cleavage is shown to be likely the result of
sequence-dependent conformational dynamics. Hence, the relative efficiency of
ultrasonic cleavage may serve as indicator of sequence specific flexibility in both strands
of DNA. Such numerical evaluation may be useful for identifying promoter regions in
genomes and for assessing the preference for nucleosome positioning. 


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Mechanochemical Cleavage of DNA by Ultrasound (pp. 1-24)