The structural organization of nuclear pre-mRNA. II. Very long double-stranded structures in nuclear pre-mRNA

High molecular weight nuclear pre-messenger RNA (pre-mRNA or hnRNA) isolated from Ehrlich ascites carcinoma cells contains besides moderately long (100--200 base pairs) snap-back double-stranded structures, also longer double-stranded structure containing at least 300--800 base pairs. Their double-stranded nature was proved by Cs2SO4 gradient centrifugation. Very long double-stranded sequences are not able to snap-back after RNA melting. While the moderately long double-stranded RNA (dsRNA) is renatured at C0t1/2 approximately equal to 5-10(-4), the very long dsRNA shows a higher complexity (C0t1/2 approximately equal to 2-10(-2). They also hybridize to less reiterated class of DNA than moderately long dsRNA. Two classes of dsRNA are represented by different sequences as followed from cross-renaturation experiments. Very long dsRNA forms stable hybrids with 20% of total poly(A)+mRNA of cytoplasm. The properties of different classes of ds structures present in nuclear pre-mRNA are compared and their possible nature is discussed. The presence of very long dsRNA may reflect either the symmetric transcription of structural genes, or the transcription from those DNA sequences which are complementary to each other but located in different parts of the genome.