High affinity interaction of mouse DNA topoisomerase I with di- and trinucleotides corresponding to specific sequences of supercoiled DNA cleaved chain

Recently mouse DNA topoisomerase I (topo) was shown to possess high affinity for a single-stranded AAGACTTAG nonanucleotide (Ki=2.0 μM) corresponding to the scissile strand of the minimal DNA duplex, which is necessary for cleavage of supercoiled DNA. In order to determine the most important part of the above sequence for the DNA recognition by topo, the interactions of the enzyme with a set of extremely short (2–5 nucleotides in length) oligonucleotides corresponding to different parts of the nonanucleotide have been investigated. The affinities of different oligonucleotides corresponding to the CTTAG part of the sequence (Ki=0.13–0.92 mM) were shown to be significantly lower than that for the AAGA tetranucleotide (Ki=9.0 μM). Topo effectively recognized even short oligonucleotides containing only two or three bases (AGA and pAG, Ki=20 and 50 μM). We suppose that oligonucleotides having a high affinity to the enzyme can offer a unique opportunity for the rational design of topoisomerase-targeting drugs.