A simple generally applicable method for measuring radioactive substances separated by polyacrylamide and agarose-gel electrophoresis

Affinity chromatographic purification of nucleosomes containing transcriptionally active DNA sequences

The unfolding of nucleosome cores in transcriptionally active chromatin uncovers the sulfhydryl groups of histone H3, making them accessible to SH-reagents. This has suggested that nucleosomes from active genes could be retained selectively on organomercurial/agarose columns. When nucleosomes released from rat liver nuclei by limited digestion with micrococcal nuclease were passed through an Hg affinity column, a run-off fraction of compact, beaded nucleosomes was separated from a retained nucleosome fraction. Although both contained monomer-length DNA and a full complement of core histones, histones in the retained fraction were hyperacetylated. Dot blot hybridizations showed the Hg-bound nucleosome fraction to be enriched in DNA sequences transcribed by hepatocytes (serum albumin and transferrin genes), while a brain-specific gene (preproenkephalin) was not retained, but appeared in the nucleosomes of the run-off fraction. The results are discussed in light of other evidence linking hyperacetylation of histones H3 and H4 to conformational changes at the middle of the nucleosome core.

Studies on (Na+ + K+)-activated ATPase. XLVI. Effect of cation-induced conformational changes on sulfhydryl group modification

(1) (Na+ + K+)-ATPase (ATP phosphohydrolase, EC 3.1.6.3) contains 34 sulfhydryl groups on the catalytic subunit, and two on the glycoprotein subunit. Under native conditions, only sulfhydryl groups on the catalytic subunit are accessible to modifying reagents. (2) The degree of inhibition of (Na+ + K+)-ATPase activity by N-ethylmaleimide and 5,5'-dithiobis(2-nitrobenzoic acid) depends on the cations present in the reaction medium. Mg2+ strongly enchances the inhibitory effects of both sulfhydryl reagents. The effects of Mg2+ on the inhibition by 5,5'-dithiobis(2-nitrobenzoic acid) are counteracted by the addition of Na+ or K+. Na+ has no more effect than choline on the inhibition by 5,5'-dithiobis(2-nitrobenzoic acid), but it enhances the inhibitory effect of N-ethylmaleimide at low Na+ concentrations (less than 10 mM). Low concentrations of K+ (less than 10 mM) slightly protect the enzyme against modification. (3) Titration of residual sulfhydryl groups reveals that these ions do not only influence modification of essential sulfhydryl groups, but also that of sulfhydryl groups which are not essential for the enzyme activity. (4) These results indicate that Na+, K+ and Mg2+ have marked effects on the conformation of the catalytic subunit of (Na+ + K+)-ATPase. Various enzyme conformations can be induced, depending on the concentration and the kind of cation added. The largest effects are observed after addition of Mg2+.

Distribution within chromatin of deoxyribonucleic acid repair synthesis occurring at different times after ultraviolet radiation

We have compared the initial distribution and subsequent redistribution within chromatin of nucleotides incorporated during the early ("rapid") phase and the late ("slow") phase of UV-induced DNA repair synthesis. As has been observed for the early repair phase, most or all of the nucleotides incorporated during the late repair phase are initially staphylococcal nuclease and DNase I "sensitive" (i.e., rapidly digested). This initial enhanced sensitivity is accompanied by both an underrepresentation of these nucleotides in the 145--165 base pari (core) DNA produced by staphylococcal nuclease digestion and an absence of these nucleotides in the approximately 20-base repeat pattern produced by DNase I digestion. Furthermore, nucleotides incorporated at late time after damage are involved in nucleosome rearrangements as reported previously for repair synthesis occurring at early times [Smerdon, M. J., & Lieberman, M. W. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 4238--4241]. The kinetics of redistribution, however, appear to be more rapid than those observed for early times. Following redistribution the average nucleosome repeat length of DNA containing repair-incorporated nucleotides is the same as that of bulk DNA regardless of the time after damage that repair occurs; also, many of these nucleotides coelectrophorese with the approximately 10-base repeat fragments generated by DNase I. The results yield a new interpretation of our previous studies [Smerdeon, M. J., Tlsty, T. D., & Lieberman, M. W. (1978) Biochemistry 17, 2377--2386] on the distribution of nucleotides incorporated at long times after UV irradiation.