Structurally Altered Substrates for DNA Topoisomerase. I. Effects of Inclusion of a Single 3′-Deoxynucleotide Within the Scissile Strand†

Abstract A partial DNA duplex containing a high efficiency topoisomerase I cleavage site was substituted singly at each of three sites with 3′-deoxyadenosine. Depending on the site of substitution, the facility of the topoisomerase I-mediated cleavage or ligation reactions was altered. Inclusion of the modified nucleoside at the 5′-end of the acceptor oligonucleotide diminished the rate of religation following substrate cleavage by the enzyme. This paper is dedicated to the memory of our friend and colleague, Prof. Tsujiaki Hata