Native DNA from sea urchin embryos contains single-stranded regions (gaps) of up to 3000 nucleotides. The longer gaps (more than 1400 nucleotides) are nonrandomly distributed and are rich in histone gene sequences, other moderately repetitive sequences, and polypyrimidines. The shorter gaps are associated with DNA replication. A method for isolation of the two classes of single-stranded DNA pieces is reported.