R.D. Sutherland, R.K. Moyzis, and N.A. Doggett
Los Alamos National Laboratory, Los Alamos, NM 87545
The distribution of Eco RI, Hind III and Eco RI/Hind III double digest sites and the distribution of (GT)n and Cot1 repetitive DNA was determined for 1843 cosmids mapping to 307 locations, 75 different somatic cell hybrid breakpoint intervals, and 25 bands on chromosome 16. The average frequency of Eco RI, Hind III and Eco RI/Hind III sites per cosmid for all 1843 cosmids was 6.87, 7.34 and 9.90 respectively. The frequency of Eco RI, Hind III and Eco RI/Hind III sites in cosmids that are most likely to be located in giemsa light bands was 6.65, 7.05, and 9.66 respectively. The frequency of Eco RI, Hind III and Eco RI/Hind III sites in cosmids that are most likely to be located in giemsa dark bands was 7.18, 7.75, 10.23 respectively. The higher frequency of Eco RI and Hind III sites in giemsa dark bands is consistent with these bands having a higher A + T content than light bands since both Eco RI and Hind III recognize restriction sites in which 4 of 6 bases are A or T.
Cotl DNA was present on an average of 5.16 Eco RI fragments (75%) and 4.93 Hind III fragments (67%) and 6.54 double digest fragments (66%) per cosmid. The frequency of Cotl positive Eco RI/Hind III and Eco RI/Hind III fragments in giemsa light bands was 5.12, 4.83, and 6.59 respectively. The frequency of Cotl positive Eco RI, Hind III and Eco RI/Hind III fragments in giemsa dark bands was 5.24, 5.04, and 6.41 respectively. (GT)n repeats were present on an average of 1.71 Eco RI fragments (25%) and 1.73 Hind III fragments (24%) and 1.85 double digest fragments (19%) per cosmid. The (GT)n repeats follow the same light and dark patterns as the other fragments. The averages are down ~0.10 for light bands and up ~0.10 for dark bands. These results suggest that Alu repeats (the predominate repeat in Cot1 DNA) are slightly more prevalent in giemsa dark bands. Supported by the US DOE (W-7405-ENG-36).