Enrichment and depletion of Hela topoisomerase I recognition sites among specific types of DNA elements

The SDS-induced nicking of DNA helix by Hela topoisomerase I in vitro has been studied by using 2.9 kb of cloned human DNA as the substrate. The frequency of nicking is increased from 1/23 (nick/nt) to 1/19 (nick/nt) when camptothecin is present in the nicking reaction. The cytotoxic drug also induces DNA nicks without the addition of SDS. Although the consensus built from DNA sequences from -20 to +20 of more than one hundred of the nicking sites only shows a preference for T at position -1, the distributions of the topoisomerae I-cleavable sites among different categories of specific DNA sequences are apparently non- random. Long stretches of tandem (CA), A, or T residues, and the GC-rich promoter region of alpha 1 globin gene are all refractory to the nicking reaction. However, the nicking frequencies of short direct repeats flanking different Alu type sequences are as high as 1/6 (nick/nt). Finally, several tandemly arranged minirepeats of the form (TxAy)z, that are usually found at the 3' ends of the primate Alu family or Kpnl family repeats, can be cleaved efficiently in a regular pattern by the enzyme. These data are discussed in terms of the mode of recognition of DNA sequences/structures by topoisomerase I, and its possible roles in the nonhomologous insertion of repetitive DNA sequences.