Biomaterial Database

Visualization of drug-nucleic acid interactions at atomic resolution. IX. Structures of two N,N-dimethylproflavine: 5-iodocytidylyl (3'-5') guanosine crystalline complexes. 1984

K K Bhandary, and T D Sakore, and H M Sobell, and D King, and E J Gabbay

Department of Radiation Biology and Biophysics, University of Rochester School of Medicine and Dentistry, New York 14642.

This paper describes two complexes containing N,N-dimethylproflavine and the dinucleoside monophosphate, 5-iodocytidylyl (3'-5') guanosine (iodoCpG). The first complex is triclinic, space group P1, with unit cell dimensions a = 11.78 A, b = 14.55 A, c = 15.50 A, alpha = 89.2 degrees, beta = 86.2 degrees, gamma = 96.4 degrees. The second complex is monoclinic, space group P21, with a = 14.20 A. b = 19.00 A, c = 20.73 A, beta = 103.6 degrees. Both structures have been solved to atomic resolution and refined by Fourier and least squares methods. The first structure has been refined anisotropically to a residual of 0.09 on 5,025 observed reflections using block diagonal least squares, while the second structure has been refined anisotropically to a residual of 0.13 on 2,888 reflections with full matrix least squares. The asymmetric unit in both structures contains two dimethylproflavine molecules and two iodoCpG molecules; the first structure has 16 water molecules (a total of 134 non-hydrogen atoms), while the second structure has 18 water molecules (a total of 136 non-hydrogen atoms). Both structures demonstrate intercalation of dimethylproflavine between base-paired iodoCpG dimers. In addition, dimethylproflavine molecules stack on either side of the intercalated duplex, being related by a unit cell translation along b and a axes, respectively. The basic structural feature of the sugar-phosphate chains accompanying dimethylproflavine intercalation in both structures is the mixed sugar puckering pattern: C3' endo (3'-5') C2' endo. This same structural information is again demonstrated in the accompanying paper, which describes a complex containing dimethylproflavine with deoxyribo-CpG. Similar information has already appeared for other "simple" intercalators such as ethidium, acridine orange, ellipticine, 9-aminoacridine, N-methyl-tetramethylphenanthrolinium and terpyridine platinum. "Complex" intercalators, however, such as proflavine and daunomycin, have given different structural information in model studies. We discuss the possible reasons for these differences in this paper and in the accompanying paper.

UI	MeSH Term	Description	Entries
D007364	Intercalating Agents	Agents that are capable of inserting themselves between the successive bases in DNA, thus kinking, uncoiling or otherwise deforming it and therefore preventing its proper functioning. They are used in the study of DNA.	Intercalating Agent,Intercalating Ligand,Intercalative Compound,Intercalator,Intercalators,Intercalating Ligands,Intercalative Compounds,Agent, Intercalating,Agents, Intercalating,Compound, Intercalative,Compounds, Intercalative,Ligand, Intercalating,Ligands, Intercalating
D008968	Molecular Conformation	The characteristic three-dimensional shape of a molecule.	Molecular Configuration,3D Molecular Structure,Configuration, Molecular,Molecular Structure, Three Dimensional,Three Dimensional Molecular Structure,3D Molecular Structures,Configurations, Molecular,Conformation, Molecular,Conformations, Molecular,Molecular Configurations,Molecular Conformations,Molecular Structure, 3D,Molecular Structures, 3D,Structure, 3D Molecular,Structures, 3D Molecular
D011370	Proflavine	Topical antiseptic used mainly in wound dressings.	3,6-Diamino Acridine,3,6-Diaminoacridine,Proflavin,Proflavine Hemisulfate,3,6 Diamino Acridine,3,6 Diaminoacridine,Acridine, 3,6-Diamino,Hemisulfate, Proflavine
D003460	Crystallization	The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)	Crystalline Polymorphs,Polymorphism, Crystallization,Crystal Growth,Polymorphic Crystals,Crystal, Polymorphic,Crystalline Polymorph,Crystallization Polymorphism,Crystallization Polymorphisms,Crystals, Polymorphic,Growth, Crystal,Polymorph, Crystalline,Polymorphic Crystal,Polymorphisms, Crystallization,Polymorphs, Crystalline
D000166	Acridines	Compounds that include the structure of acridine.	Acridine
D001665	Binding Sites	The parts of a macromolecule that directly participate in its specific combination with another molecule.	Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D015226	Dinucleoside Phosphates	A group of compounds which consist of a nucleotide molecule to which an additional nucleoside is attached through the phosphate molecule(s). The nucleotide can contain any number of phosphates.	Bis(5'-Nucleosidyl)Oligophosphates,Bis(5'-Nucleosidyl)Phosphates,Deoxydinucleoside Phosphates,Dinucleoside Diphosphates,Dinucleoside Monophosphates,Dinucleoside Oligophosphates,Dinucleoside Tetraphosphates,Dinucleoside Triphosphates,Bis(5'-Nucleosidyl)Tetraphosphate,Dinucleoside Polyphosphates,Diphosphates, Dinucleoside,Monophosphates, Dinucleoside,Oligophosphates, Dinucleoside,Phosphates, Deoxydinucleoside,Phosphates, Dinucleoside,Polyphosphates, Dinucleoside,Tetraphosphates, Dinucleoside,Triphosphates, Dinucleoside
D015394	Molecular Structure	The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.	Structure, Molecular,Molecular Structures,Structures, Molecular