Visualization of Drug-Nucleic Acid Interactions at Atomic Resolution. IV. Structure of an Aminoacridine/Dinucleoside Monophosphate Crystalline Complex, 9-Aminoacridine: 5-Iodocytidylyl(3'-5')Guanosine

摘要

9-Aminoacridine forms a crystalline complex with the dinucleoside monophosphate, 5-iodocytidylyl(3'-5')guanosine (iodoCpG). These crystals are monoclinic, space group P2 sub 1 , with a = 13.98 A, b = 30.58 A, c = 22.47 A and beta = 113.9. The structure has been solved to atomic resolution by Patterson and Fourier methods, and refined by a combination of Fourier and sum function Fourier methods. The asymmetric unit contains four 9-aminoacridine molecules, four iodoCpG molecules and 21 water molecules, a total of 245 atoms. 9-Aminoacridine demonstrates two different intercalative binding modes and, along with these, two slightly different intercalative geometries in this model system. The first of these is very nearly symmetric, the 9-amino- group lying in the narrow groove of the intercalated base-paired nucleotide structure. The second shows grossly asymmetric binding to the dinucleotide, the 9-amino- group lying in the wide groove of the structure. Associated with these two different intercalative binding modes is a difference in geometries in the structures. Although both structures demonstrate C3' endo (3'-5') C2' endo mixed sugar puckering patterns, with corresponding twist angles between base-pairs of about 10 exp 0 , they differ in the magnitude of the helical screw axis dislocation accompanying intercalation. In the pseudosymmetric intercalative structure, this value is about +0.5 A, whereas in the asymmetric intercalative structure this value is about +2.7 A. These conformational differences can be best described as a sliding of base-pairs on the intercalated acridine molecule. (ERA citation 04:039244)