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

Technical Report · Mon Jan 01 04:00:00 EST 1979

DOI:https://doi.org/10.2172/6065153· OSTI ID:6065153

Sakore, T. D.; Reddy, B. S.; Sobell, H. M.

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/sup 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.

• Research Organization: Rochester Univ., NY (USA)
• DOE Contract Number: EY-76-C-02-3490
• OSTI ID: 6065153
• Report Number(s): UR-3490-1573
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
400301* -- Organic Chemistry-- Chemical & Physicochemical Properties-- (-1987)
ACRIDINES
AZINES
BOND LENGTHS
CHEMICAL BONDS
COMPLEXES
CRYSTAL STRUCTURE
HETEROCYCLIC COMPOUNDS
MOLECULAR STRUCTURE
NUCLEOSIDES
NUCLEOTIDES
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PYRIDINES
RIBOSIDES