Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Structural Features of A-T Oligomers Studied by X-ray Crystallography

We reported some time ago (1) that the oligonucleotide d(ATATAT) crystallizes as a duplex with Hoogsteen base pairing. In an effort to find related structures, we have undertaken the study of oligonucleotides which only contain adenine and thymine in different sequences. Practically no data are available on crystal structures of this type. We have obtained crystal data on twelve additional sequences with different lengths (6 to 14 base pairs). Most of them have comparatively low resolution (3 to 6 Å), probably related to the high hydration observed. Nevertheless we have been able to determine their basic features in the crystals, which belong to two families:
    a. Coiled-coils: observed in the alternating oligonucleotides d(AT)5 and d(AT)6. The latter structure has been recently described in detail (2). Both appear to show Hoogsteen base-pairs.

    b. Pseudohexagonal stacks of infinite columns of duplexes with no apparent lateral interactions. In several cases we have found that the unit cells contain many duplexes (up to 17) in the direction of the helical axis. In general, Watson-Crick base-pairs are present in these crystals.
These two different types of crystal organization had never been found before in oligonucleotide crystals.

References and Footnotes
  1. Abrescia, N. G. A., Thompson, A., Huynh-Dinh, T. and Subirana, J. A. Proc. Natl. Acad. Sci. USA 99, 2806-2811 (2002).
  2. Campos, J. L., Urpí, L., Sanmartín, T., Gouyette, C. and Subirana, J. A. Proc. Natl. Acad. Sci. USA 102 In press (2005).

L. Urpi1
J. L. Campos1
N. Valls1,*
T. Sanmartín1
E. Alechaga1
R. Baldini1
D. De Luchi1
M. Richter1
A. Santaolalla1
C. Gouyette2
J. A. Subirana1

1Department of Chemical Engineering
Universitat Politecnica de Catalunya
Av. Diagonal 647
E-08028 Barcelona, Spain
2Unite de Chimie Organique
Institut Pasteur
28, rue du Doctor Roux
F-75724 Paris, France

*Phone: 34+934016685
Fax: 34+934010978
Email: nuria.valls@upc.edu