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A H-NMR Study of the DNA Binding Characteristics of Thioformyldistamycin, an Amide Isosteric Lexitropsint Malvinder P. Singh,* Surat Kumar,* Tomi Joseph,* Richard T. Pon,s and J. William Lawn*-* Department zyxwvutsr of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada, and Regional DNA Synthesis Laboratory, University of Calgary, Calgary, Alberta T2N 4N1, Canada Received December 20,1991; Revised Manuscript Received April zyxw 15, I992 ABSTRACT: The interaction of thioformyldistamycin, an amide isostere of the naturally occurring antibiotic distamycin A, with a self-complementary decadeoxynucleotide duplex, d(CGCAATTGCG)2, has been examined using a variety of high-field 'H-NMR techniques. The ligand exhibits two forms in solution arising from geometric isomerism due to restricted rotation around the thioformamide bond. Only the thermo- dynamically more stable Z-form is shown to bind to the oligonucleotide along its minor groove at the central 5'-AATT segment with the end groups of the ligand extending into the flanking GC regions but without any close contact at the amidinium terminus. Cross-peaks involving characteristic intra- and interresidue proton connectivities in the 2D experiments (COSY and NOESY) were employed to assign individual resonances of both strands in the asymmetric DNA-drug complex. The solution structure of the complex was zyxwvutsrq constructed by molecular mechanics calculations based upon initial estimates of drug-DNA NOE contacts and further refined through energy minimization. These results complement previous structural studies on distamycin and other lexitropsins zyxwvut with oligonucleotides. The exchange of the ligand between two equivalent binding sites on the DNA sequence was estimated to occur at 40 s-' with a free energy of activation of 16.5 kcal-mol-' at 321-326 K. There was no evidence of formation of a 2:l drug-oligomer complex, in contrast to the case of the natural product, which is attributed to steric demands of the larger sulfur atom. s e v e r a l compounds including distamycin A (Arcamone et al., 1967; Hahn, 1975), netropsin (Julia & Preau-Joseph, 1963), anthelvencin A (Probst et al., 1965), noformycin (Diana, 1973), and the kikumycins A and B (Takahishi et al., 'This investigation was supported by a grant (to J.W.L.) from the Address correspondence to this author. t University of Alberta. 8 University of Calgary. National Cancer Institute of Canada. 1972) comprise the pyrrole amidine class of antitumor anti- biotics. These oligopeptides appear to share a common mo- lecular mechanism of binding to double-stranded B-DNA (Wartell et al., 1974) and are known to inhibit the DNA and RNA polymerase activity in vitro through interactions with the DNA template, thereby blocking the synthesis of DNA (Hahn, 1980; Zimmer et al., 1971,1983). Both distamycin A and netropsin have been of widespread interest in bio- chemical and biophysical investigations, and the reader is directed to extensive reviews on such studies (Hahn, 1980; 0006-2960/92/043 1-6453$03.00/0 zyxwvu 0 1992 American Chemical Society