Visualization of Drug-Nucleic Acid Interactions at Atomic Resolution. VII. Structure of an Ethidium/Dinucleoside Monophosphate Crystalline Complex, Ethidium: Uridylyl(3′-5′)Adenosine

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Abstract
Ethidium forms a crystalline complex with the dinucleoside monophosphate, uridylyl (3′-5′) adenosine (UpA). The complex crystallizes in the monoclinic space group P2, with unit cell dimensions, a = 13.704 Å, b = 31.674 Å, c = 15.131 Å β = 113.9°. This light atom structure has been solved to atomic resolution and refined by full matrix least squares to a residual of 0.12, using 3,034 observed-reflections. The asymmetric unit consists of two ethidium molecules, two UpA molecules and 19 solvent molecules, a total of 145 non-hydrogen atoms. The two UpA molecules are hydrogen-bonded together by Watson-Crick type base pairing. Base-pairs in this duplex are separated by 6.7 Å; this reflects intercalative binding by one of the ethidium molecules. The other ethidium molecule stacks on either side of the intercalated base-paired dinucleoside monophosphate, being related by a unit cell translation along the a axis. The conformation of the sugar-phosphate backbone accompanying intercalation has been accurately determined in this analysis, and contains the mixed sugar-puckering pattern: C3′ endo (3′-5′) C2′ endo. This same structural feature has been observed in the ethidium-iodoUpA and ethidium-iodoCpG complexes, and exists in two additional structures containing ethidium-CpG. Taken together, these studies confirm our earlier sugar-puckering assignments and demonstrate that iodine covalently bound to the C5 position on uridine or cytosine does not alter the basic sugar-phosphate geometry or the mode of ethidium intercalation in these model studies. We have proposed this stereochemistry to explain the intercalation of ethidium (as well as other simple intercalators) into both DNA and into double-helical RNA, and discuss this aspect of our work further in this paper and in the accompanying papers.