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J Mol Biol 135: 483-500 (1979)[80140504]

Different regions of a complex statellite DNA vary in size and sequence of the repeating unit.

M. Carlson & D. Brutlag

The 1.688 g/cm3 satellite DNA of Drosophila melanogaster is composed primarily of 359 base-pair units repeated in tandem. Most of these units contain a single cleavage site for both HaeIII and Hinfl restriction endonucleases; however, some units lack one or both sites. Previously we had shown that the distribution of HaelIl and HinfI endonuclease sites varies widely between different regions of 1.688 g/cm3 satellite DNA; for example, some regions contain HaelIl sites in every unit and other regions (>10,000 base-pairs) contain no HaeIII sites (Carlson & Brutlag, 1977). We have flow cloned molecules of 1.688 g/cm3 satellite DNA which lack HaeIII sites and have shown that the absence of sites is caused by sequence variation rather than base modification. This result indicates that regions of 1-688 g/cm3 satellite DNA with different distributions of restriction sites differ in the sequence of their repeating units. We also show that a large fraction of the satellite DNA which is not cleaved by HaelIl endonuclease still contains HinfI endonuclease sites (and AluI sites) spaced about 359 base-pairs apart. However, one cloned segment lacking HaelIl sites was found to contain 33 tandem copies of a novel 254 base-pair unit. Sequence analysis showed that this 254 base-pair unit is homologous to the 359 repeat except for a 98 base-pair deletion. These data suggest that both units have evolved from a common ancestor and that each has subsequently become amplified into separate tandem arrays.

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