HIGH-AFFINITY INTERACTION OF MOUSE DNA-TOPOISOMERASE-I WITH DINUCLEOTIDES AND TRINUCLEOTIDES CORRESPONDING TO SPECIFIC SEQUENCES OF SUPERCOILED DNA CLEAVED CHAIN

Recently mouse DNA topoisomerase I (topo) was shown to possess high af finity for a single-stranded AAGACTTAG nonanucleotide (K-i = 2.0 mu M) corresponding to the scissile strand of the minimal DNA duplex, which is necessary for cleavage of supercoiled DNA. In order to determine t he most important part of the above sequence for the DNA recognition b y 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 seq uence (K-i = 0.13-0.92 mM) were shown to be significantly lower than t hat for the AAGA tetranucleotide (K-i = 9.0 mu M). Topo effectively re cognized even short oligonucleotides containing only two or three base s (AGA and pAG, K-i = 20 and 50 mu M). We suppose that oligonucleotide s having a high affinity to the enzyme can offer a unique opportunity for the rational design of topoisomerase-targeting drugs. (C) 1997 Fed eration of European Biochemical Societies.