An NMR study of the covalent and noncovalent interactions of CC-1065 and DNA

Abstract

The binding of the antitumor drug CC-1065 has been studied with nuclear magnetic resonance (NMR) spectroscopy. This study involves two parts, the elucidation of the covalent binding site of the drug to DNA and a detailed investigation of the noncovalent interactions of CC-1065 with a DNA fragment through analysis of 2D NOE (NOESY) experiments. A CC-1065-DNA adduct was prepared, and an adenine adduct was released upon heating. NMR (1H and 13C) analysis of the adduct shows that the drug binds to N3 of adenine by reaction of its cyclopropyl group. The reaction pathway and product formed were determined by analysis of the 13C DEPT spectra. An octamer duplex, d(CGATTAGC.GCTAATCG), was synthesized and used in the interaction study of CC-1065 and the oligomer. The duplex and the drug-octamer complex were both analyzed by 2D spectroscopy (COSY, NOESY). The relative intensity of the NOEs observed between the drug (CC-1065) and the octamer duplex shows conclusively that the drug is located in the minor groove, covalently attached to N3 of adenine 6 and positioned from the 3'----5' end in relation to strand A [d(CGATTA6GC)]. A mechanism for drug binding and stabilization can be inferred from the NOE data and model-building studies.

High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA

“…Prior characterization of complexes of ()-CC-1065 with a DNA duplex (Scahill et al, 1990) and duocarmycin A with both a hairpin DNA triplex and duplex (Lin & Patel, 1992;1995) have provided insight into some of the non-covalent interactions stabilizing the ligand in the DNA minor groove. Herein we report the high resolution solution structure of a DNA duplex alkylated by duocarmycin SA (Figure 2).…”

Cooperative Bending of the 21-Base-Pair Repeats of the SV40 Viral Early Promoter by Human Sp1

“…The biological activity of (+)-CC-1065 stems fromitsability toalkylateN3 ofadenine on duplex DNA in a sequence-selective manner and modify the structure and local conformation of DNA (Hurley & Draves, 1993). Previous studies from this laboratory, in collaboration with scientists from The Upjohn Company, have shown that (+)-CC-1065 lies in the minor groove of duplex DNA covering a 4-5-bp region to the 5' side of modified adenine (Hurley et al, 1984;Reynolds et al, 1985;Scahill et al, 1990). As a consequence of formation of the (+)-CC-l065-(N3)-adenine adduct, (+)-CC-1065 induces bending, winding, and stiffening of the DNA (Lee et al, 1991;Sun & Hurley, 1992).…”

Sequence-specific arrest of primer extension on single-stranded DNA by an oligonucleotide-minor groove binder conjugate.

“…NMR analysis has shown that bound CC-1065 spans [5][6] bp in the minor groove of DNA (26). By analogy, a conjugated CDPI3 group probably occupies a similar length of minor groove, with the region of interaction displaced 1-2 bp away from the site of conjugation.…”

“…Communicated by Robert L. Letsinger, Northwestern University, Evanston, IL, December 26,1995 ABSTRACT A minor groove binder (MGB) derivative (N-3-carbamoyl-1,2-dihydro-3H-pyrrolo [3,2- (9), "peptide nucleic acids" (10), C-5-propynyl-containing ODNs (11), 2'-O-methyl-ODNs (12), and N3'-P5'-phosphoramidate ODNs (13).…”