Single-stranded regions in DNA isolated from different developmental stages of the sea urchin

Long-term labeled sea urchin embryo (Strongylocentrotus purpuratus) DNAs were examined for size of recovered pieces, single-strandedness, and length of continuous double-stranded regions. Sizing on neutral sucrose gradients indicates that morula stage DNA sediments predominantly at 31 S, blastula stage DNA at 27 S, and gastrula stage DNA as a broad range of sizes of greater than 29 S. Treatment of [3H]thymidine-labeled DNA with Aspergillus oryzae S1 nuclease removes 19% of the 3H from morula stage DNA, 4% of the 3H from blastula stage DNA, and less than 0.1% of the 3H from gastrula stage DNA. Sedimentation of S1 nuclease treated [3H]DNAs on alkaline sucrose gradients indicates that in native morula stage DNA there is a nick or gap in one strand approximately every 9700 base pairs, in native blastula stage DNA about every 3300 base pairs, and very few nicks or gaps in native gastrula stage DNA.