Visualization of drug-nucleic acid interactions at atomic resolution. VII. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: uridylyl(3'-5')adenosine
Ethidium forms a crystalline complex with the dinucleoside monophosphate, uridylyl (3'-5') adenosine (UpA). The complex crystallizes in the monoclinic space group P2/sub 1/ with unit cell dimensions, a = 13.704 A, b = 31.674 A, c = 15.131 A, ..beta.. = 113.8/sup 0/. This light atom structure has been solved to atomic resolution and refined by full matrix least squares to a residual of 0.12, using 3034 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 base pairing. Base-pairs in this duplex are separated by 6.7 A; 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 the authors 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. The authors have proposed this stereochemistry to explain the intercalation of ethidium into both DNA and into double-helical RNA. 15 references, 10 figures, 2 tables.
- Research Organization:
- Univ. of Rochester, NY (USA)
- OSTI ID:
- 6619338
- Journal Information:
- J. Biomol. Struct. Dyn.; (United States), Vol. 1:5
- Country of Publication:
- United States
- Language:
- English
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Related Subjects
NUCLEIC ACIDS
BIOCHEMICAL REACTION KINETICS
POLYCYCLIC AROMATIC AMINES
MOLECULAR STRUCTURE
ADENOSINE
AZAARENES
COVALENCE
EXPERIMENTAL DATA
LEAST SQUARE FIT
MOLECULES
STEREOCHEMISTRY
STRUCTURAL MODELS
AMINES
AROMATICS
DATA
HETEROCYCLIC COMPOUNDS
INFORMATION
KINETICS
MAXIMUM-LIKELIHOOD FIT
NUCLEOSIDES
NUCLEOTIDES
NUMERICAL DATA
NUMERICAL SOLUTION
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
REACTION KINETICS
RIBOSIDES
550200* - Biochemistry