Visualization of drug-nucleic acid interactions at atomic resolution. VII. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: uridylyl(3'-5')adenosine

Journal Article · Sun Jan 01 04:00:00 EST 1984 · J. Biomol. Struct. Dyn.; (United States)

DOI:https://doi.org/10.1080/07391102.1984.10507510· OSTI ID:6619338

Jain, S C; Sobell, H M

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), Journal Name: J. Biomol. Struct. Dyn.; (United States) Vol. 1:5; ISSN JBSDD
• Country of Publication: United States
• Language: English

Related Subjects

550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
ADENOSINE
AMINES
AROMATICS
AZAARENES
BIOCHEMICAL REACTION KINETICS
COVALENCE
DATA
EXPERIMENTAL DATA
HETEROCYCLIC COMPOUNDS
INFORMATION
KINETICS
LEAST SQUARE FIT
MAXIMUM-LIKELIHOOD FIT
MOLECULAR STRUCTURE
MOLECULES
NUCLEIC ACIDS
NUCLEOSIDES
NUCLEOTIDES
NUMERICAL DATA
NUMERICAL SOLUTION
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
POLYCYCLIC AROMATIC AMINES
REACTION KINETICS
RIBOSIDES
STEREOCHEMISTRY
STRUCTURAL MODELS