The binding of poly (rA) and poly (rU) to denatured DNA. II. Studies with natural DNAs

Purine base composition analysis of normal and tumor rat DNA

Chemical and viral induced rat tumors were analyzed for their purine base composition and compared to normal tissue DNA'S. The tumors were induced by 7,12-dimethylbenz[a]anthracene (DMBA), 20-methylcholanthrene (MC), 3,4-benzopyrene (BP), 1,2-dimethylhydrazine (DMH) and Rous sarcoma virus (RSV). Normal DNAs were extracted from colon, caecum, liver, spleen and embryo and used as reference standards for base composition of normal rat DNA. The composition of purines was obtained by spectrophotometric estimation of the total adenine and guanine (A/G) contents after depurination of the DNA with 66% formic acid at 30 degrees C for 18 h and passage over a cationic exchange resin. Statistical comparison of the A/G molar ratios in normal rat DNAs (1.271) to those of chemical-induced primary tumors (1.342) has shown a highly significant increase. No significant differences could be detected when the base composition of the normals were compared to transplanted tumors, whether chemically or virally induced. Possible explanations from a mutational point of view are discussed.

Electrophoretic strand separation of long DNAs with poly (U,G) in agarose gels

We have found that binding of poly(U,G) to single-stranded DNA decreases its mobility in 0.3% agarose gels. Differential binding to the complementary strands of denatured duplex DNA provides a simple method for strand separation. The method is shown to work with bacteriophage lambda DNA, adenovirus DNA and mtDNA for Tetrahymena pyriformis. In all cases the strand that binds more poly(U,G) in CsCl gradients also binds more in gels. The separated strands can be directly blotted from the gel onto nitrocellulose filters and used for hybridization experiments.

Prevention of G:C pairing in mouse DNA by complete blocking of guanine residues with glyoxal. Availability of cytosine, adenine and thymine for hydrogen bonding with added unmodified polynucleotides

We have developed conditions for the reaction of single-stranded DNA with glyoxal which permit blocking of essentially all guanine residues. This procedure effectively prevents base pairing involving these guanine residues, yet permits cytosine, thymine and adenine residues in the DNA to pair with added polynucleotides. Modification of DNA with glyoxal greatly reduces intrastrand helical regions, resulting in a very low binding to hydroxyapatite, as compared to unmodified DNA. Annealing of modified DNA with some synthetic polynucleotides of restricted composition (but not others) leads to a significant increase in binding, presumably because mouse DNA has sequences not containing guanine which are capable of hydrogen bonding to the added polynucleotides. This relatively simple procedure may allow isolation and further study of these guanine-free sequences in DNA.

The presence of (dA.dT)20-25 tracts in the DNA of primitive eukaryotes

Previous work by Jacobson et al. (1) has shown that the number and distribution of (dA.dT)25 tracts in the nuclear DNA of the slime mold Dictyostelium discoideum reflects the number and the distribution of transcriptional units. To investigate whether this is a general phenomenon we compared the nuclear DNAs of other primitive eukaryotes with respect to their content of large (dA.dT)n tracts via the thermal stability of their hybrids with poly(rA). The results of our analysis indicate that all nuclear DNAs tested have (dA.dT)20-25 tracts, but the frequency of such tracts varies from one per 5.4 X 10(6) daltons in Dictyostelium nuclear DNA to one per 2.8 X 10(8) daltons in Crithidia luciliae nuclear DNA. We conclude that the presence of (dA.dT)20-25 tracts is not an obligatory characteristic of the transcriptional unit in primitive eukaryotes. Chromatography of native DNAs on poly(rU) Sephadex columns shows that the large (dA.dT)n tracts occurring in the genomes of both primitive and higher eukaryotes are widely distributed throught these genomes.