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Nucleic Acids Research, 1988, Vol. 16, No. 16 7975-7993
© 1988

Articles

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

Carlos Perez-Stable+, Chein Celia Shen and Che-Kun Shen*

Department of Genetics, University of California, Davis CA 95616, USA

+Present address: Department of Human Genetics sad Development, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA

*To whom correspondence should be addressed

Received April 8, 1988. Revised July 11, 1988. Accepted July 11, 1988.

The SDS-induced nicking of DNA helix by Hela topoisomerase I in vitro haa 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 tham 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 C globin gene are all refractory to the nicking reaction. Howevar, 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 (TA), that are usually found at the 3' ends of the primate Alu family xKpynll 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 seqeunces/structures by topoisomerase I, and its possible roles in the nonhomologous insertion of repetitive DNA sequences.


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