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

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Abstract
A long (147 base pairs), natural A.T rich polypyrimidine/ polypurine tract has been found 55 base pairs downstream of a chicken embryonic nyosin heavy chain (MHC) gene. Analysis at the nucleotide level of nicks induced by S1 and Naurospora crassa nucleases indicate that this long interrupted polypyrimidine/polypurine tract exists in an alternate DNA structure in vitro at pH4.5 and pH7.5 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.