Spacing of polypyrimidine regions in mouse DNA as determined by poly(adenylate,guanylate) binding

The DNA from many higher organisms contains unexpectedly long runs of pyrimidine nucleotides (polypyrimidines). In mouse cells, these range in size from about 25 to 250 nucleotides and account for about 0.5% of the total DNA. They contain both thymine and cytosine in close to equimolar amounts but few or none are pure thymine or cytosine runs. When native DNA from mouse cells was banded in a CsCl gradient, polypyrimidines were part of DNA molecules of all base compositions. This indicates that, unlike Drosophila melanogaster DNA (Birnboim & Sederoff, 1975), they are not clustered as a satellite component. A procedure for isolating fragments of single-stranded DNA which contain polypyrimidines has been developed. Polypyrimidine sites in DNA are complexed with poly(A,G) and the DNA/poly(A,G) complex is bound to hydroxyapatite. The percentage of DNA which binds is a function of its chain length. A maximum of 60% of the DNA was bound, at lengths of > 15 × 10³ bases². We conclude that polypyrimidine sites are distributed throughout the majority of the mouse genome at intervals of 12 to 15 × 10³ bases.