A long polypyrimidine/polypurine tract induces an altered DNA conformation on the 3' coding region of the adjacent myosin heavy chain gene

A long (147 base pairs), natural A.T rich polypyrimidine/polypurine tract has been found 55 base pairs downstream of a chicken embryonic myosin heavy chain (MHC) gene. Analysis at the nucleotide level of nicks induced by S1 and Neurospora crassa nucleases indicate that this long interrupted polypyrimidine/polypurine tract exists in an alternate DNA structure in vitro at pH 4.5 and pH 7.5 in both supercoiled and linear plasmid DNA. The polypyrimidine/polypurine tract induces this alternate structure upon at least 200 base pairs of its 5' flanking DNA, and thus extends into the 3' coding and non-coding regions of the neighboring MHC gene. The different nicking patterns induced by the nucleases S1 and N. crassa on each strand of this alternate structure suggests that the polypyrimidine/polypurine tract may form heteronomous DNA. When this long polypyrimidine/polypurine tract is present in a supercoiled plasmid at low pH, a new and as yet undefined S1 hypersensitive DNA alteration was detected near the center of this tract.