Two classes of single-stranded regions in DNA from sea urchin embryos

Oligodeoxynucleotides capable of binding to GC-rich regions in DNA are inappropriately synthesized during random hexanucleotide-primed labeling reactions

Random hexanucleotide labeling is a commonly used and powerful technique for preparing radiolabeled nucleic acid probes. Because of the dependence of DNA polymerase upon single-stranded DNA as a template, the technique should theoretically also be useful for detecting small amounts of single-stranded DNA in the presence of a larger amount of double-stranded DNA. In the course of such an experiment, we identified an unexpected reaction that could contribute to background problems often encountered during Southern and Northern blotting. In the complete absence of template, random hexanucleotides appear capable of functioning both as template as well as primer, giving rise to labeled oligonucleotides as large as 20-mers. Some of these bind very tightly to GC-rich regions in target DNA immobilized on membranes, resisting high-stringency washing conditions. By choosing shorter incubation times and including sufficient single-stranded template, the problem may be minimized.

Sizing of single-stranded regions in double-stranded DNA by preparative benzoylated DEAE-cellulose chromatography

The concentration of caffeine required to elute wholly single-stranded DNA from benzoylated DEAE-cellulose is proportional to the polynucleotide length. The use of benzoylated DEAE-cellulose chromatography for isolating and sizing single-stranded regions in double-stranded DNA has been examined using a series of hybrid molecules. Restriction fragments of the replicating form of bacteriophage luminal diameter X174 were hybridized to the intact 'plus' strand, thereby forming hybrids having single- and/or double-stranded regions in the kilobase range. A series of such hybrid preparations were subject to caffeine concentration gradient elution from benzoylated DEAE-cellulose. After logarithmic transformation, a linear relationship (R = 0.94) could be demonstrated between eluting caffeine concentration and single-stranded length, irrespective of the length of associated double-stranded regions or the location, within a given fragment, of unpaired nucleotides. Benzoylated DEAE-cellulose chromatography may therefore be used to separate and characterize, on a preparative scale, double-stranded DNA containing single-stranded regions.

Replication forks are underrepresented in chromosomal DNA of Xenopus laevis embryos

Chromosomal DNA was isolated from rapidly dividing cells of Xenopus laevis embryos at blastulation, at gastrulation, and at the beginning of hatching. Few, if any, replication forks were seen by electron microscopy in DNA isolated at any stage of embryogenesis. Instead, unbranched DNA, which appeared to be single-stranded, was abundant at all stages. The percentage of chromosomal DNA that was single-stranded was quantitated by electron microscopy and by monitoring the release of acid-soluble radioactivity during digestion of labeled chromosomal DNA with nucleases specific for single-stranded DNA. The amount of single-stranded DNA was inversely correlated with the length of S phase during embryogenesis. We postulate that chromosomal DNA replication in X. laevis embryos takes place by a mechanism in which strand separation is uncoupled from DNA synthesis.