Issue December 2009

category image Volume 27
No. 3 (p 245-398)
December 2009
ISSN 0739-110

Ultrasonic Cleavage of Nicked DNA (p. 391-398)

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.

I.A. IlŽicheva1
D.Yu. Nechipurenko2
S.L. Grokhovsky1,*

1Engelhardt Institute of Molecular Biology
RAS, Vavilov str. 32
Moscow 119991, Russia
2Dep. of Physics
Moscow State University
Moscow 119992, Russia

*Phone: 499 135 97 18
Fax: 499 135 14 05
grok@imb.ac.ru

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