Deproteinization with phenol of alternating polydeoxyadenylate-deoxythymidylate and other DNA-like polymers

The binding of benzo(a)pyrene to DNA components of differing sequence complexity

An examination has been made of the binding, both in vitro and in vivo, of the benzo(a)pyrene (BP) adduct to DNA components of differing sequence complexity. Annealing was performed at low renaturation temperatures in the presence of high concentrations of formamide to minimize hydrocarbon-induced depurination. BHK-DNA was modified in vitro using a tritiated derivative of the ultimate carcinogenic metabolite of BP, 7alpha,8beta-di-hydroxy-9beta,10beta-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE). Co-renaturation of this modfied DNA with [14C]-thymidine-labelled BHK-DNA demonstrated that the hydrocarbon adduct did not interfere with strand annealing and showed that the BP adduct was distributed randomly throughout all DNA sequence classes. However, when the DNA of cells in culture was modified by [3H]BP, following metabolic activation, and mixed with [14C]-thymidine-labelled DNA, a small but reproducible difference in the renaturation of the two labels was found. This difference in renaturation profiles was not due to base-compositional effects since a similar result was found when the alternate 14C-label was present in guanine bases, the principal site of BP modification. The small difference in the renaturation of the two radioactive labels indicated an enrichment of the hydrocarbon on the most rapidly-renaturing sequence components (the palindromic and highly repetitive sequences) where it amounted to between 19 and 64% increased modification.

Isolation of A-T-rich fragments from calf thymus DNA using the phenol method

The action of phenol on the products of partial digestion of calf thymus DNA by K2 DNAase causes a loss of 3--5% of the material passing into the phenol phase. This part of DNA can be regained in the aqueous phase by lowering both the temperature and the ionic strength. Among oligonucleotides up to 7 monomers in length, those which are soluble in phenol do not contain guanine residues. Phenol-soluble DNA fragments of the molecular weight of an order of 2000--50,000 appeared to be composed mainly of adenosine phosphate. They also contain some thymine and only traces of guanine and cytosine. Some longer A-T-rich fragments, even up to 5-10(6) daltons, were repeatedly found in the phenol phase, but their base composition has not been determined yet. The method presented here was found very convenient for the isolation of relatively large A-T-rich DNA fragments. The property of DNA or its fragments to dissolve in phenol seems to be dependent on an adequate primary structure, probably similar to that of poly (dA-dT).

Factors influencing the yield of satellite DNA in extractions from Drosophila virilis and Drosophila melanogaster adults and embryos

The application of different DNA extraction methods to identical batches of Drosophila virilis and Drosophila melanogaster flies or embryos has revealed that the ionic strength of a homogenization medium is of critical importance if chloroform extractions are performed. The low yield of satellite DNA after homogenization in low salt buffers is less severe if EDTA is included in the buffer. Phenol extraction procedures result in no such differential behavior of satellite and main band DNA, but under certain circumstances a particular satellite fraction of Drosophila virilis DNA may be lost.

A polynucleotide segment rich in adenylic acid in the rapidly-labeled polyribosomal RNA component of mouse sarcoma 180 ascites cells

The rapidly-labeled polyribosomal RNA component from mouse sarcoma 180 cells is retained on nitrocellulose (Millipore) membrane-filters at high ionic strength. This property is due to the presence of a polynucleotide sequence rich in adenylic acid that resists both T(1) and pancreatic RNase digestion. The resistant material shows sedimentation characteristics close to those of transfer RNA. The RNA molecules that contain this material can be separated from the rest of the polysomal RNA by differential phenol extraction with neutral and alkaline Tris buffers. Synthetic poly(A) exhibits the same behavior as the rapidly-labeled polysomal RNA with respect to Millipore binding and phenol fractionation. The characteristics of the rapidly-labeled polysomal RNA component permit its isolation free of ribosomal RNA.