We describe a method that permits the study of the state of cytosine methylation and of in vivo protein-DNA interactions in higher eukaryotes. This powerful technique is applicable to any gene of interest at the single-copy level. To study DNA methylation, the total uncloned genomic DNA, digested with a restriction endonuclease is subjected to a cytosine-specific hydrazine reaction and chemical cleavage. The DNA fragments of interest are linearly amplified with Taq polymerase and a sequence-specific radioactivity labeled synthetic primer. Following amplification, the DNA fragments are separated on a sequencing gel that is directly autoradiographed. To study protein-DNA interactions in vivo, we use a similar method, except that the DNA of interest is isolated from cells treated either with dimethyl sulfate or UV light. The resolution power of this technique is demonstrated by two examples, which have been studied previously by the conventional methods of genomic sequencing and "footprinting."