Specificity of DNA cleavage by ultrasound

Abstract

Cleavage of double-stranded DNA fragments with known nucleotide sequences upon sonication at 22 and 44 kHz was studied by PAGE. The cleavage rate was shown to depend on the fragment size, pH, ionic strength, and temperature. Double-strand breaks occurred preferentially in 5'-CpG-3' dinucleotides. The strand was broken between C and G so that the phosphate group was at the 5' side of G in the products. The cleavage rate proved to depend on the sequences flanking the cleavage site. The character of cleavage changed in the presence of Pt-bis-netropsin, a sequence-specific ligand that alters the local conformation of DNA.[PUBLICATION ABSTRACT]