Mechanochemical Cleavage of DNA by Ultrasound» in "Advances in Engineering Researchстатья

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Дата последнего поиска статьи во внешних источниках: 17 февраля 2016 г.

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[1] Mechanochemical cleavage of dna by ultrasound in advances in engineering research / S. L. Grokhovsky, I. A. Il’icheva, D. Y. Nechipurenko et al. // Advances in Engineering Research. — Vol. 8. — Nova Science Publishers ISSN: 2163-3932. ISBN: 978-1-63321-282-4 New-York, 2014. — P. 213–236. 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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