Visualization of drug-nucleic acid interactions at atomic resolution. X. Structure of a N,N-dimethylproflavine: deoxycytidylyl(3'-5')deoxyguanosine crystalline complex
N,N-dimethylproflavine forms a crystalline complex with deoxycytidylyl(3'-5')deoxyguanosine (d-CpG), space group P2/sub 1/,2/sub 1/2, with a = 21.37 A, b = 34.05 A, c = 13.63 A. The structure has been solved to atomic resolution and refined by Fourier and least squares methods to a residual of 0.18 of 2032 observed reflections. The structure consists of two N,N-dimethylproflavine molecules, two deoxycytidylyl (3'-5')deoxyguanosine molecules and 16 water molecules, a total of 128 nonhydrogen atoms. As with other structures of this type, N,N-dimethylproflavine molecules intercalate between base-paired d-CpG dimers. In addition, dimethylproflavine molecules stack on either side of the intercalated duplex, being related by a unit cell translation along the c axis. Both sugar-phosphate chains demonstrate the mixed sugar puckering geometry: C3' endo (3'-5') C2' endo. The same intercalative geometry has been seen in two other complexes containing N,N-dimethylproflavine and iodoCpG, described in the accompanying paper. Taken together, these studies indicate a common intercalative geometry present in both RNA- and DNA- model systems. Again, N,N-dimethylproflavine behaves as a simple intercalator, intercalating asymmetrically between guanine-cytosine base-pairs. The free amino- group on the intercalated dimethylproflavine molecule does not hydrogen bond directly to the phosphate oxygen. Other aspects of the structure will be presented. 4 references, 5 figures, 2 tables.
- Research Organization:
- Univ. of Rochester School of Medicine and Dentistry, NY
- OSTI ID:
- 5358006
- Journal Information:
- J. Biomol. Struct. Dyn.; (United States), Vol. 1:5
- Country of Publication:
- United States
- Language:
- English
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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
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Related Subjects
62 RADIOLOGY AND NUCLEAR MEDICINE
NUCLEOSIDES
X-RAY DIFFRACTION
PROFLAVINE
COMPLEXES
CONFIGURATION INTERACTION
CRYSTALLOGRAPHY
ELECTRONIC STRUCTURE
STRUCTURAL CHEMICAL ANALYSIS
ACRIDINES
AMINES
AROMATICS
AZAARENES
AZINES
COHERENT SCATTERING
DIFFRACTION
FLAVINES
HETEROCYCLIC COMPOUNDS
MUTAGENS
NUCLEOTIDES
ORGANIC COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PYRIDINES
RIBOSIDES
SCATTERING
550200* - Biochemistry
550602 - Medicine- External Radiation in Diagnostics- (1980-)