Organization of highly repeated sequences in mouse main-band DNA

Abstract

Renaturation analysis shows that the main CsCl density band of mouse DNA (at 400 bases mol. wt) contains a minimum of four second-order kinetic components: non-repetitive DNA; two major classes of repeated DNA, called “moderately repeated” and “highly repeated”, each comprising 8 to 16% of the genome; and a minor sub-class of the highly repeated DNA, about 0·5% of the genome with a satellite-like complexity. The highly repeated main-band sequences are isolated from high molecular weight DNA (12,000 bases) by renaturation to low C 0 t § and hydroxyapatite chromatography. This DNA is spread for electron microscopy by the formamide isodenaturing technique. Most of the bimolecular renaturation products show interspersion of renatured and single-stranded regions. The renatured regions average about 700 base-pairs in length, most being in the range of 200 to 1000. On molecules where two or more renatured regions. The renatured regions average about 700 base-pairs in length, most being in the range of 200 to 1000. On molecules where two or more renatured regions can be identified, they are separated by a wide range of distances averaging 1800 bases. A minority fraction (about 12% by weight) of the bimolecular renaturation products shows no evidence of interspersion, and may consist of tandemly repeated sequences. The renaturation rate of the highly repeated DNA fraction (at initial mol. wts of 6000 and 12,000 bases) is studied before and after shearing the DNA to low molecular weight. The kinetic complexity of the interspersed, single-stranded DNA that is attached to renatured, highly repeated DNA is thereby determined. Most of the unrenatured DNA contains highly repeated sequences similar in complexity to the sequences that renatured at low C 0 t . Only about 20% of the interspersed DNA has a low repetition frequency, approximately non-repetitive. We conclude that about 15% of the mouse main-band DNA contains highly repeated sequences, most of which are organized as permuted tandem repeats. About 5% of the non-repetitive DNA of mouse is interspersed with this fraction of the genome. This model of sequence organization differs from those that have been demonstrated for more moderately repeated sequences of higher organisms, where much more non-repetitive DNA is interspersed with the repeated sequences.