Isolation of a mouse DNA fraction which encodes more informational than non informational RNA sequences

A small fraction of single-stranded DNA (ssDNA), amounting to 1.5--2% of the total DNA, was isolated from native nuclear DNA of mouse Ascites tumour cells. In RNA-driven annealing reactions, 40--42% of the ssDNA, (labelled with [3H]-thymidine or 125I) could be hybridized to cytoplasmic RNA was compared with 4--4.5% for the non repetitious component of bulk DNA and 60--63% of the ssDNA could be hybridized to nuclear RNA as compared with 20--22% for bulk DNA. It was also found that most of the ssDNA sequences which are hybridizable to homologous RNA, consisted of non self-reassociating DNA regions (which can be reassociated with non repetitious bulk DNA). These findings complete earlier data obtained in other cell systems and demonstrate that ssDNA mainly originates from active DNA transcription sites which encode informational RNA sequences. It is proposed that ssDNA is formed via selective endogenous nuclease attacks presumably at an early stage of the DNA purification procedure.