Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Crystalline DNA Structures Stabilized by Transition Metals

Transition metals such as Co2+ and Ni2+ have been shown to play a very important role in the stabilisation of oligonucleotide structures. Several structures have been solved by X-ray crystallography in the presence of these ions (1-4). They show a clear affinity with the terminal guanines interacting specifically with their N7 atoms. Different modes of binding have been found which involve different packing roles for these ions:
  1. Interaction with the N7 of either paired or flipped out guanines (Fig. 1A).
  2. Acting as a bridge between two flipped out guanines of two different oligonucleotide columns in the crystal (Fig. 1B, 1C). The guanine planes can be organized perpendicular or parallel. As a result the orientation of the oligonucleotide columns varies in each case.
  3. Interaction between two columns through a guanine of one duplex and a phosphate of a different duplex (Fig. 1D).
  4. Hydrated ions may also stabilize the crystals by conventional electrostatic interactions.
The importance of these kinds of interactions is apparent in the crystal structures solved, as they clearly help to stabilize crystal packing. Furthermore they show new ways to build DNA nanostructures.

Figure 1: A. Interaction of two duplexes in one oligonucleotide column. B. Interaction of a Co2+ ion with the N7 of two guanines. C. A Co2+ ion bridging two parallel oligonucleotide columns. D. Guanine-Ni2+-phosphate interactions between two columns.

References and Footnotes
  1. Valls, N., Wright, G., Steiner, R. A., Murshudov, G. N., and Subirana, J. A. Acta. Cryst. D60, 680-685 (2004).
  2. Valls, N., Uson, I., Gouyette, C., and Subirana, J. A. J. Am. Chem. Soc. 126, 7812-7816 (2004).
  3. Yang, X.-l., Robinson, H., Gao, Y.-G., and Wang, A. H.-J. Biochemistry 39, 10950-10957 (2000).
  4. Abrescia, N. G. A., Malinina, L., Fernández, L. G., Huynh-Dinh, T., Neidle, S., and Subirana, J. A. Nucleic Ac. Res. 27, 1593-1599 (1999).

N. Valls*
J. A. Subirana

Department of Chemistry
Politechnical University of Catalunya
Av. Diagonal 647
08028 Barcelona, Spain

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