Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1978 Nov;5(11):4417–4422. doi: 10.1093/nar/5.11.4417

A 1:2 crystalline complex of ApA:proflavine: a model for binding to single-stranded regions in RNA.

S Neidle, G Taylor, M Sanderson
PMCID: PMC342758  PMID: 724521

Abstract

The structure of a 1"2 complex of adenylyl-(3',5')-adenosine phosphate and proflavine hemisulfate has been determined using the methods of x-ray crystallography. Since the ApA does not form a mini double helix, it may serve as a model for the interaction of planar molecules with single stranded nucleic acids. The dinucleotide adopts an extended conformation with the adenines in adjacent molecules forming base pairs. A most unusual feature of the molecule is that it does not obey the "rigid nucleotide" concept although none of the torsion angles occur in energetically unfavourable regions. This is most probably due to the strong interactions between the proflavine and the oligonucleotide.

Full text

PDF
4419

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Alden C. J., Arnott S. Visualization of planar drug intercalations in B-DNA. Nucleic Acids Res. 1975 Oct;2(10):1701–1717. doi: 10.1093/nar/2.10.1701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Berman H. M., Neidle S., Stodola R. K. Drug-nucleic acid interactions: conformational flexibility at the intercalation site. Proc Natl Acad Sci U S A. 1978 Feb;75(2):828–832. doi: 10.1073/pnas.75.2.828. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Camerman N., Fawcett J. K., Cameran A. Molecular structure of a deoxyribose-dinucleotide, sodium thymidylyl-(5' yields to 3')-thymidylate-(5') hydrate (pTpT), and a possible structural model for polythymidylate. J Mol Biol. 1976 Nov 15;107(4):601–621. doi: 10.1016/s0022-2836(76)80086-1. [DOI] [PubMed] [Google Scholar]
  4. Crick F. H., Klug A. Kinky helix. Nature. 1975 Jun 12;255(5509):530–533. doi: 10.1038/255530a0. [DOI] [PubMed] [Google Scholar]
  5. Jack A., Klug A., Ladner J. E. "Non-rigid" nucleotides in tRNA: a new correlation in the conformation of a ribose. Nature. 1976 May 20;261(5557):250–251. doi: 10.1038/261250a0. [DOI] [PubMed] [Google Scholar]
  6. Jack A., Ladner J. E., Klug A. Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5A resolution. J Mol Biol. 1976 Dec 25;108(4):619–649. doi: 10.1016/s0022-2836(76)80109-x. [DOI] [PubMed] [Google Scholar]
  7. Jain S. C., Tsai C. C., Sobell H. M. Visualization of drug-nucleic acid interactions at atomic resolution. II. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodocytidylyl (3'-5') guanosine. J Mol Biol. 1977 Aug 15;114(3):317–331. doi: 10.1016/0022-2836(77)90253-4. [DOI] [PubMed] [Google Scholar]
  8. Kallenbach N. R., Berman H. M. RNA structure. Q Rev Biophys. 1977 May;10(2):138–236. doi: 10.1017/s0033583500000202. [DOI] [PubMed] [Google Scholar]
  9. LERMAN L. S. Structural considerations in the interaction of DNA and acridines. J Mol Biol. 1961 Feb;3:18–30. doi: 10.1016/s0022-2836(61)80004-1. [DOI] [PubMed] [Google Scholar]
  10. Neidle S., Achari A., Taylor G. L., Berman H. M., Carrell H. L., Glusker J. P., Stallings W. C. Structure of a dinucleoside phosphate--drug complex as model for nucleic acid--drug interaction. Nature. 1977 Sep 22;269(5626):304–307. doi: 10.1038/269304a0. [DOI] [PubMed] [Google Scholar]
  11. Quigley G. J., Rich A. Structural domains of transfer RNA molecules. Science. 1976 Nov 19;194(4267):796–806. doi: 10.1126/science.790568. [DOI] [PubMed] [Google Scholar]
  12. Quigley G. J., Seeman N. C., Wang A. H., Suddath F. L., Rich A. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles. Nucleic Acids Res. 1975 Dec;2(12):2329–2341. doi: 10.1093/nar/2.12.2329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. RICH A., DAVIES D. R., CRICK F. H., WATSON J. D. The molecular structure of polyadenylic acid. J Mol Biol. 1961 Feb;3:71–86. doi: 10.1016/s0022-2836(61)80009-0. [DOI] [PubMed] [Google Scholar]
  14. Seeman N. C., Day R. O., Rich A. Nucleic acid-mutagen interactions: crystal structure of adenylyl-3',5'-uridine plus 9-aminoacridine. Nature. 1975 Jan 31;253(5490):324–327. doi: 10.1038/253324a0. [DOI] [PubMed] [Google Scholar]
  15. Stout C. D., Mizuno H., Rubin J., Brennan T., Rao S. T., Sundaralingam M. Atomic coordinates and molecular conformation of yeast phenylalanyl tRNA. An independent investigation. Nucleic Acids Res. 1976 Apr;3(4):1111–1123. doi: 10.1093/nar/3.4.1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Sussman J. L., Kim S. H. Idealized atomic coordinates of yeast phenylalanine transfer RNA. Biochem Biophys Res Commun. 1976 Jan 12;68(1):89–96. doi: 10.1016/0006-291x(76)90014-0. [DOI] [PubMed] [Google Scholar]
  17. Sussman J. L., Kim S. Three-dimensional structure of a transfer rna in two crystal forms. Science. 1976 May 28;192(4242):853–858. doi: 10.1126/science.775636. [DOI] [PubMed] [Google Scholar]
  18. Sussman J. L., Seeman N. C., Kim S. H., Berman H. M. Crystal structure of a naturally occurring dinucleoside phoaphate: uridylyl 3',5'-adenosine phosphate model for RNA chain folding. J Mol Biol. 1972 May 28;66(3):403–421. doi: 10.1016/0022-2836(72)90423-8. [DOI] [PubMed] [Google Scholar]
  19. Tsai C. C., Jain S. C., Sobell H. M. Visualization of drug-nucleic acid interactions at atomic resolution. I. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium:5-iodouridylyl (3'-5') adenosine. J Mol Biol. 1977 Aug 15;114(3):301–315. doi: 10.1016/0022-2836(77)90252-2. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES