[A new method of studying DNA conformation by chemical modification]

A new method of discrimination of double-stranded (ds) and single-stranded (ss) regions in DNA molecules has been developed. It makes use of two alkylating reagents, a voluminous and a small-sized, the former being sensitive to the DNA conformation. A bulky reagent, N,N,N'-tri(beta-chloroethyl)-N'-(p-formylphenyl) propylendiamine-1,3 (TFP), was used to detect the hairpin structure in the palindrome-containing DNA fragment 373 nucleotides long prepared from the ds EcoRI-BamHI fragment of the plasmid pBR322. The fragment was modified by TFP and cleaved by piperidine at the alkylated guanine residues according to the Maxam-Gilbert procedure. Guanine residues in the hairpin formed by palindrome were protected from the TFP action, while dimethylsulfate modified all guanines. Application of the method for the identification of loops, stem-and-loop structures, and unwinded regions of DNA is discussed.