Ultrasonic cleavage of nicked DNA.

Structural properties of nicked dsDNA have been an object of numerous studies due to their special role in reparation processes. Here we report experimental results covering ultrasound irradiation of a nicked dsDNA fragments. We have quantitatively estimated ultrasonic cleavage rates in these fragments using the polyacrylamide gel electrophoresis. Data reveal cleavage enhancement in the regions of about 10 b. p. up and down the nick. The intensity of ultrasonic cleavage near the nick is one order of magnitude higher than intensity of ultrasonic cleavage in the same sites of the intact dsDNA fragments. At the same time, the cleavage rates in positions beyond the regions around the nick markedly grow weak comparing to the sequence-specific cleavage rates of intact dsDNA. Thus, the presence of the nick serves as an expressive structural alteration which exceeds any modulation of the structure caused by the base-pair sequence.