Sequence Composition of Rat Ascites Chromosomal Ribonucleic Acid

A population of chromatin-associated low molecular weight RNA molecules (cRNA) prepared from rat Novikoff ascites cells hybridizes to a minimum of 16% of isolated middle repetitive and a minimum of 1% of isolated single copy rat DNA as measured in solution. This sums to about 4.0% hybridization of total DNA. In solution the rate of hybridization of cRNA to isolated middle repetitive DNA is approximately that expected if 80-100% of the cRNA consists of middle repetitive transcripts. In contrast cRNA hybridizes to about 4.7 % of total rat DNA immobilized on filters at a rate at least 100 times slower than that predicted from the solution hybridization, suggesting that steric or geometric effects are considerable in this type of assay. In a solution hybridization reaction to total DNA, present in excess, at least 50% of the cRNA hybridizes at an average rate similar to the major component of the middle repetitive DNA. The T_m of cRNA, hybridized to filter-bound DNA, is at least 12° lower than native DNA. The lowering of T_m may be due, in part, to base-pair mismatch and, in part, to the shortness of the hybrids.