Nucleotide specificity in DNA scission by neocarzinostatin

Using the DNA sequencing technique of Maxam and Gilbert, we show that the protein antibiotic neocarzinostatin, cleaves double-stranded phiX174 DNA restriction fragments almost exclusively at deoxythymidylic and deoxyadenylic acid residues in a reaction requiring 2-mercaptoethanol. Overall, deoxythymidylic acid residues are attacked much more frequently than are deoxyadenylic acid residues, although there is variability in the attack rate for both nucleotides at different locations in the DNA molecule. While all deoxythymidylic acid residues are sites of scission by neocarzinostatin, not all deoxyadenylic acid residues are cleavage sites. There appears to be no clear-cut nucleotide sequence specificity in determining cleavage frequency. Single-stranded DNA is a very poor substrate for neocarzinostatin-induced scission; with one single-stranded DNA fragment, cleavage occurs at a position that is not attacked in double-stranded DNA. The possible significance for its biological activity of a drug that can attack both members of a DNA base pair is discussed.