A distinct intron-DNA structure in simian virus 40 T-antigen and adenovirus 2 E1A genes

Distinct structures delineating the introns of simian virus 40 T-antigen and adenovirus 2 E1A genes have been discovered. The structures, which are centered around the branch points of the genes inserted in supercoiled double-stranded plasmids, are specifically targeted through photoactivated strand cleavage by the metal complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III). The DNA sites that are recognized lack sequence homology but are similar in demarcating functionally important sites on the RNA level. The single-stranded DNA fragment corresponding to the coding strand of the E1A gene was also found to fold into a structure apparently identical to that in the supercoiled E1A gene based on the recognition by the metal complex. Further investigation of different single-stranded DNA fragments showed that the structure requires the sequences at both ends of the intron plus the flanking sequences but not the middle of the intron. These results provide direct evidence that the positions of these introns are structurally encoded on the DNA level.