Skip Navigation

This Article
Right arrow Print PDF (7173K)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (23)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Bingman, C.
Right arrow Articles by Sundaralingam, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bingman, C.
Right arrow Articles by Sundaralingam, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 1992, Vol. 20, No. 24 6637-6647
© 1992

STRUCTURAL BIOLOGY

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

Craig Bingman1,3,+, Sanjeev Jain1,§, Gerald Zon2 and Muttaiya Sundaralingam1,3,*

1Crystallography Laboratory, Department of Biochemistry, University of Wisconsin Madison, WI 53706, USA 2Applied Biosystems 850 Lincoln Centre Drive, Foster City, CA 94404, USA 3Laboratory of Biological Macromolecular Structure, Department of Chemistry and Ohio State Biotechnology Center, The Ohio State University 1060 Carmack Road, Columbus, OH 43210-1002, USA

*To whom correspondence should be addressed

Received August 28, 1992. Revised November 18, 1992. Accepted November 18, 1992.

The crystal structure of the alternating dodecamer d(GCGTACGTACGC) (5'-GC) has been determined to a resolution of 2.55Å using oscillation film data. The crystals belong to space group P61 22, a=b=46.2Å, c=71.5Å 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°, in the direction of the major groove compared to 20° 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.

+Present address: Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA

§Present address: Department of Biochemistry, St Louis University, St Louis, MO 63104, USA


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
D. Jose and D. Porschke
Dynamics of the B-A transition of DNA double helices
Nucleic Acids Res., April 23, 2004; 32(7): 2251 - 2258.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.