A long-range and two short-range periodicities are superimposed in the 1.706-g/cm3 satellite DNA from calf thymus.

Abstract

The organization of repetitive sequences has been studied by restriction nuclease analysis of satellite DNAs from calf thymus. Several novel structural features have been found in the 1.706-g/cm3 satellite DNA (satellite III). A long-range periodicity of 2350 base pairs detected by cleavage with restriction endonucleases Bsp or EcoRII and two short-range periodicities of approximately 22 and 11 base pairs found by digestion with restriction endonucleases Alu and Sau, respectively, are superimposed in the nucleotide sequence of this satellite DNA. About 14% of the DNA present in long-range repeats lack the short-range periodicities. The lenght of the long-range repeats varies by multiples of approximately 22 base pairs. The distribution of the restriction sites in the satellite DNA is non-random. The evolution of this satellite DNA is not adequately explained by saltatory amplification and random divergence alone; unequal crossing-over and additional non-random processes are discussed. In the 1.723-g/cm3 satellite DNA (satellite II) a periodicity of 45 base pairs has been found by cleavage with restriction endonuclease Alu. The cleavage pattern of this satellite DNA is compatible with a 3% random divergence of an originally homogeneous nucleotide sequence. A physical map has been established for the 1.715-g/cm3 satellite DNA (satellite I) containing the cleavage sites of restriction endonucleases Alu, Sau, Pst, and EcoRI. A periodicity of 1400 base pairs (Alu, Sau, EcoRI) and of 700 base pairs (Pst) has been observed in the nucleotide sequence of this satellite DNA. φX174 replicative form I DNA fragments of known sequence have been used to calibrate the sizes of the fragments in restriction nuclease digests of mouse, BSC-1, and the three calf satellite DNAs. The monomeric and oligomeric fragments derived from these satellite DNAs by limit or partial digestion provide overlapping sets of size standards for DNA fragments from 20 up to 20000 base pairs.