Amplified ribosomal DNA from Xenopus laevis has heterogeneous spacer lengths

Eco R(1) restriction endonuclease makes two cuts in each repeating unit of amplified ribosomal DNA (rDNA) from Xenopus laevis. The locations of these cuts have been established by comparison of the secondary structure of single-stranded Eco R(1) fragments (as visualized in the electron microscope) with that of X. laevis rRNAs and of long strands of uncut rDNA. Of the two classes of fragments generated, the smaller one contains 90% of the 28S rRNA gene, has a duplex molecular weight of 3.0 x 10(6) and is homogeneous in size. The larger class of molecules contains 80% of the 18S rRNA gene and all of the nontranscribed spacer. These latter fragments are heterogeneous with molecular weights ranging from 4.0 to 5.9 x 10(6). The distribution of sizes within the large class of fragments varies among different preparations of rDNA, and heterogeneity is present in the DNA amplified from the rDNA of a single nucleolar organizer. The heterogeneity is located in the nontranscribed spacer region which is variable in length. This has been demonstrated by the formation of deletion loops in heteroduplexes made between larger fragments of different lengths.