Periodicity of exonuclease III digestion of chromatin and the pitch of deoxyribonucleic acid on the nucleosome.

Exonuclease III has previously been shown to pause about every 10 nucleotides along the 3' strands while it invades the nucleosome core. Here, the exact periodicity of this digestion, i.e., the spacing of the pauses, was determined. Results showed that the exonuclease digests the first 20 nucleotides at the edge of the nucleosome core with a periodicity of approximately 11 nucleotides; in contrast, DNA closer to the center of the particle is digested with a smaller periodicity of about 10 nucleotides. These figures differ from the known periodicity of DNase I digestion, approximately 10 and 10.5 nucleotides at the edge and in the center of the nucleosome, respectively. Moreover, as shown by sedimentations in sucrose gradients, the structure of the nucleosome does not appear to be significantly altered by the gradual destruction of its DNA moiety by the exonuclease. Such stability of the nucleosome, along with other complementary observations, indicates that the transition in the digestion periodicity of the exonuclease may not be the consequence of a structural rearrangement of the particle upon trimming. This transition may rather be ascribed to the properties of the native nucleosome and to the intrinsic mechanism of action of the enzyme. Finally, evidence is presented which suggests that the exonuclease 10-nucleotide periodicity of digestion of the inner region of the nucleosome reflects a 10 base pair/turn pitch of the DNA in that region.