Ultrasonic Cleavage of DNA: Quantitative Analysis of Sequence Specificity

Looking for new means of assessing local conformational and dynamic heterogeneities in DNA structure, we have estimated the rates of phosphodiester bond cleavage in DNA fragments of known sequence caused by ultrasonic treatment. Among the 16 dinucleotide steps possible, those with 5′-ward cytosine [5′-d(CpN)-3′] are distinguished by significantly higher cleavage rates: CG > CA = CT > CC. The possible causes of this intriguing phenomenon are considered.