Binding of 9-aminoacridine to bulged-base DNA oligomers from a frame-shift hot spot
- 13 December 1988
- journal article
- research article
- Published by American Chemical Society (ACS) in Biochemistry
- Vol. 27 (25) , 8904-8914
- https://doi.org/10.1021/bi00425a006
Abstract
Complexes of 9-aminoacridine and two derivatives with oligomers based on the sequence of a hot spot for frame-shift mutations, 5''dGATGGGGCAG, are investigated by proton NMR and equilibrium dialysis. Competition dialysis experiments show that the drug binds bulge-containing oligomers more strongly than regular duplexes of similar sequence and length, with one apparent strong site. A duplex containing an extra cytidine in a run of C''s has the highest affinity for 9-aminoacridine among the sequences tested. An oligomer containing five consecutive G .cntdot. C pairs shows cooperative drug binding, indicating that G tracts of this length may have an altered helical structure. Complexes of a regular 8-mer and a 9-mer containing a bulged guanosine are examined in detail by two-dimensional NMR techniques. 9-Aminoacridine preferentially binds at TpG sites in the 8-mer but binds primarily at the bulged guanosine in the G-bulge 9-mer. Drug-DNA NOE''s in the 8-mer complex are compared with with the crystal structure of 9-aminoacridine and 5-iodo-CpG [Sakore et al. (1979) J. Mol. Biol, 135, 763-785]. The NMR data suggest that the drug intercalates across the base pairs of both strands with the amino group projecting into the minor groove.This publication has 18 references indexed in Scilit:
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