Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 Dec 25;20(24):6637–6647. doi: 10.1093/nar/20.24.6637

Crystal and molecular structure of the alternating dodecamer d(GCGTACGTACGC) in the A-DNA form: comparison with the isomorphous non-alternating dodecamer d(CCGTACGTACGG).

C Bingman 1, S Jain 1, G Zon 1, M Sundaralingam 1
PMCID: PMC334581  PMID: 1480485

Abstract

The crystal structure of the alternating dodecamer d(GCGTACGTACGC) (5'-GC) has been determined to a resolution of 2.55A using oscillation film data. The crystals belong to space group P6(1) 22, a = b = 46.2A, c = 71.5A with one strand in the asymmetric unit, and are isomorphous with a previously described non-alternating dodecamer, d(CCGTACGTACGG) (5'-CC). Refinement by X-PLOR/NUCLSQ gave a final R factor of 14.2% for 1089 observations. The molecule adopts the A-DNA form. The interchange of the terminal base pairs in the two dodecamers results in differences in the intermolecular contacts and may account for the differences in the bending. This dodecamer shows an axial deflection of 30 degrees, in the direction of the major groove compared to 20 degrees in 5'-CC and may be a consequence of additional contacts generated in 5'-GC by the interchange of end base pairs. The high helical axis deflection appreciably influences the local helical parameters. The molecule exhibits relatively high inclination angles, and has a narrow major groove. The helical parameters when described relative to the dyad-related hexamer halves of the molecule give more reasonable values. The crystal packing, local helical parameters, torsion angles, and hydration are described and also compared with the non-alternating 5'-CC dodecamer.

Full text

PDF
6647

Selected References

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

  1. Bingman C. A., Zon G., Sundaralingam M. Crystal and molecular structure of the A-DNA dodecamer d(CCGTACGTACGG). Choice of fragment helical axis. J Mol Biol. 1992 Oct 5;227(3):738–756. doi: 10.1016/0022-2836(92)90221-5. [DOI] [PubMed] [Google Scholar]
  2. Brennan R. G., Westhof E., Sundaralingam M. Structure of a Z-DNA with two different backbone chain conformations. Stabilization of the decadeoxyoligonucleotide d(CGTACGTACG) by [Co(NH3)6]3+ binding to the guanine. J Biomol Struct Dyn. 1986 Feb;3(4):649–665. doi: 10.1080/07391102.1986.10508453. [DOI] [PubMed] [Google Scholar]
  3. Chandrasekaran R., Wang M., He R. G., Puigjaner L. C., Byler M. A., Millane R. P., Arnott S. A re-examination of the crystal structure of A-DNA using fiber diffraction data. J Biomol Struct Dyn. 1989 Jun;6(6):1189–1202. doi: 10.1080/07391102.1989.10506544. [DOI] [PubMed] [Google Scholar]
  4. Fairall L., Martin S., Rhodes D. The DNA binding site of the Xenopus transcription factor IIIA has a non-B-form structure. EMBO J. 1989 Jun;8(6):1809–1817. doi: 10.1002/j.1460-2075.1989.tb03575.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Heinemann U., Lauble H., Frank R., Blöcker H. Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC). Nucleic Acids Res. 1987 Nov 25;15(22):9531–9550. doi: 10.1093/nar/15.22.9531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Jain S., Sundaralingam M. Effect of crystal packing environment on conformation of the DNA duplex. Molecular structure of the A-DNA octamer d(G-T-G-T-A-C-A-C) in two crystal forms. J Biol Chem. 1989 Aug 5;264(22):12780–12784. [PubMed] [Google Scholar]
  7. Jain S., Zon G., Sundaralingam M. Base only binding of spermine in the deep groove of the A-DNA octamer d(GTGTACAC). Biochemistry. 1989 Mar 21;28(6):2360–2364. doi: 10.1021/bi00432a002. [DOI] [PubMed] [Google Scholar]
  8. Otwinowski Z., Schevitz R. W., Zhang R. G., Lawson C. L., Joachimiak A., Marmorstein R. Q., Luisi B. F., Sigler P. B. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 1988 Sep 22;335(6188):321–329. doi: 10.1038/335321a0. [DOI] [PubMed] [Google Scholar]
  9. Quadrifoglio F., Manzini G., Yathindra N. Short oligodeoxynucleotides with d(G-C)n sequence do not assume left-handed conformation in high salt conditions. J Mol Biol. 1984 May 25;175(3):419–423. doi: 10.1016/0022-2836(84)90358-9. [DOI] [PubMed] [Google Scholar]
  10. Takusagawa F. The crystal structure of d(GTACGTAC) at 2.25 A resolution: are the A-DNA's always unwound approximately 10 degrees at the C-G steps? J Biomol Struct Dyn. 1990 Feb;7(4):795–809. doi: 10.1080/07391102.1990.10508524. [DOI] [PubMed] [Google Scholar]
  11. Westhof E., Dumas P., Moras D. Crystallographic refinement of yeast aspartic acid transfer RNA. J Mol Biol. 1985 Jul 5;184(1):119–145. doi: 10.1016/0022-2836(85)90048-8. [DOI] [PubMed] [Google Scholar]

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

RESOURCES