EFFECTS OF BASE MUTATIONS ON TOPOISOMERASE-II DNA CLEAVAGE STIMULATED BY MAMSA IN SHORT DNA OLIGOMERS

DNA cleavage by topoisomerase II in the absence or presence of mAMSA, and VM-26 was investigated in a series of oligonucleotides of 36 and 42 base pairs, which were derived from the DNA sequence of the major topoisomerase II cleavage site in the matrix-associated region of SV40 DNA. Topoisomerase II introduced strand cuts at several sites in the oligonucleotides, and the sequence selectivities of DNA cleavage with and without drugs were the same as in larger SV40 DNA fragments. A time course analysis showed that mAMSA specifically stimulated DNA cleavage at the 4263/4266 site, while DNA cleavage was specifically induced at the 4265/4268 site by the enzyme without drug or with VM-26. In agreement with recent findings on local nucleotide requirements in order for mAMSA to stimulate DNA cleavage, the 4263/4266 site had adenines at the two positions +1. This nucleotide requirement was challenged by mutating the bases 4263 and 4266 of the oligonucleotide representing the natural SV40 DNA sequence. New cleavage sites were not observed in the mutated oligonucleotides, and base mutations had an effect on DNA cleavage induced with and without the two drugs. This general effect was likely due to the sensitivity of topoisomerase II itself to the local DNA sequence. Nevertheless, effects of base mutations were more pronounced for mAMSA than for VM-26. Point mutations of either base 4263 or 4266, representing the two positions +1, reduced markedly the stimulative effect of DNA cleavage at the 4263/4266 site by mAMSA, and mutations of both bases completely abolised it. The effects of these base mutations on DNA cleavage at other sites varied depending on the site and the mutated base. In particular, a purine at position -2 of the 4265/4268 site increased cleavage at that site by the enzyme without drugs. A guanine at position +2 tended to favor topoisomerase II DNA cleavage with the studied drugs. A pyrimidine at position -1 of the 4259/4262 site allowed the stimulative effect of DNA cleavage by mAMSA at the site, while a purine did not. The results indicate that the dinucleotide cleaved by topoisomerase II is crucial for stimulation of DNA cleavage by mAMSA and that the in vitro DNA binding and cleavage by topoisomerase II is determined by nucleotides immediately surrounding the cleavage site.