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Literature DB >> 7355129

The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.

H S Shieh, H M Berman, M Dabrow, S Neidle.

Abstract

A 2:2 complex of proflavine and deoxycytidylyl-3', 5'-guanosine has been crystallized and its structure determined by x-ray crystallography. The two dinucleoside phosphate strands form self complementary duplexes with Watson Crick hydrogen bonds. One proflavin is asymmetrically intercalated between the base pairs and the other is stacked above them. The conformations of the nucleotides are unusual in that one strand has C3',C2'endomixed sugar puckering and the other has C3',C3' endo deoxyribose sugars. These results show that the conformation of the 3'sugar is of secondary importance to the intercalated geometry.

Entities: Chemical

Mesh：

Substances：

Year: 1980 PMID： 7355129 PMCID： PMC327244 DOI： 10.1093/nar/8.1.85

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

15 in total

1. "Non-rigid" nucleotides in tRNA: a new correlation in the conformation of a ribose.

Authors: A Jack; A Klug; J E Ladner
Journal: Nature Date: 1976-05-20 Impact factor: 49.962

2. RNA double-helical fragments at atomic resolution. I. The crystal and molecular structure of sodium adenylyl-3',5'-uridine hexahydrate.

Authors: N C Seeman; J M Rosenberg; F L Suddath; J J Kim; A Rich
Journal: J Mol Biol Date: 1976-06-14 Impact factor: 5.469

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

Authors: S C Jain; C C Tsai; H M Sobell
Journal: J Mol Biol Date: 1977-08-15 Impact factor: 5.469

4. Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction.

Authors: S Neidle; A Achari; G L Taylor; H M Berman; H L Carrell; J P Glusker; W C Stallings
Journal: Nature Date: 1977-09-22 Impact factor: 49.962

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

Authors: C C Tsai; S C Jain; H M Sobell
Journal: J Mol Biol Date: 1977-08-15 Impact factor: 5.469

6. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation.

Authors: C Altona; M Sundaralingam
Journal: J Am Chem Soc Date: 1972-11-15 Impact factor: 15.419

7. Visualization of drug-nucleic acid interactions at atomic resolution. III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions.

Authors: H M Sobell; C C Tsai; S C Jain; S G Gilbert
Journal: J Mol Biol Date: 1977-08-15 Impact factor: 5.469

8. Stereochemical model for proflavin intercalation in A-DNA.

Authors: C J Alden; S Arnott
Journal: Nucleic Acids Res Date: 1977-11 Impact factor: 16.971

9. Visualization of planar drug intercalations in B-DNA.

Authors: C J Alden; S Arnott
Journal: Nucleic Acids Res Date: 1975-10 Impact factor: 16.971

10. Mutagen-nucleic acid intercalative binding: structure of a 9-aminoacridine: 5-iodocytidylyl(3'-5')guanosine crystalline complex.

Authors: T D Sakore; S C Jain; C C Tsai; H M Sobell
Journal: Proc Natl Acad Sci U S A Date: 1977-01 Impact factor: 11.205

15 in total

1. Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes.

Authors: G Hummer; A E García; D M Soumpasis
Journal: Biophys J Date: 1995-05 Impact factor: 4.033

2. Grand canonical ensemble Monte Carlo simulation of the dCpG/proflavine crystal hydrate.

Authors: H Resat; M Mezei
Journal: Biophys J Date: 1996-09 Impact factor: 4.033

Review 3. DNA structure and perturbation by drug binding.

Authors: S Neidle; L H Pearl; J V Skelly
Journal: Biochem J Date: 1987-04-01 Impact factor: 3.857

4. A molecular model for proflavine-DNA intercalation.

Authors: S Neidle; L H Pearl; P Herzyk; H M Berman
Journal: Nucleic Acids Res Date: 1988-09-26 Impact factor: 16.971

5. Molecular modelling of the interactions of tetra-(4-N-methylpyridyl) porphin with TA and CG sites on DNA.

Authors: K G Ford; L H Pearl; S Neidle
Journal: Nucleic Acids Res Date: 1987-08-25 Impact factor: 16.971

6. Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world.

Authors: Eric D Horowitz; Aaron E Engelhart; Michael C Chen; Kaycee A Quarles; Michael W Smith; David G Lynn; Nicholas V Hud
Journal: Proc Natl Acad Sci U S A Date: 2010-03-08 Impact factor: 11.205

7. Cooperative effects in water-biomolecule crystal systems.

Authors: J M Goodfellow
Journal: Proc Natl Acad Sci U S A Date: 1982-08 Impact factor: 11.205

8. Molecular mechanical studies of proflavine and acridine orange intercalation.

Authors: A Dearing; P Weiner; P A Kollman
Journal: Nucleic Acids Res Date: 1981-03-25 Impact factor: 16.971

9. Crystal structures of Λ-[Ru(phen)₂dppz]²⁺ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes.

Authors: Hakan Niyazi; James P Hall; Kyra O'Sullivan; Graeme Winter; Thomas Sorensen; John M Kelly; Christine J Cardin
Journal: Nat Chem Date: 2012-06-24 Impact factor: 24.427

10. Enantiomeric discrimination of chiral organic salts by chiral aza-15-crown-5 ether with C 1 symmetry: experimental and theoretical approaches.

Authors: Safak Özhan Kocakaya; Yılmaz Turgut; Necmettin Pirinççioglu
Journal: J Mol Model Date: 2015-02-21 Impact factor: 1.810