Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

The solution structure of the Holliday Junction and other branched nucleic acids: Identification of Sequence Features that determine Conformer Selection

Branched nucleic acids play important roles in the living cell and its parasites. The Holliday junction, a four-way junction, is the central intermediate in both homologous and site-specific recombination. Three-way junctions are a recurring motif in RNA and arise in DNA during recombination and replication involving phages and viruses. Proteins that recognize their targets structure-specifically interact with these branched nucleic acids. Three-way and four-way junctions can undergo a folding process that is dependent on the local sequence around the junction and on the ionic strength of the solution.

We will present high-resolution solution structures of the Holliday junction as well as of DNA three-way junction(s) (1,2). These structures were derived in part using novel NMR methodology (3). We present experimental and theoretical structural data on the multi-valent ion binding to these and other junctions (4,5). The structural data of these and other junctions have been analyzed in detail. The sequence features which determine conformation selection have been identified. For DNA three-way junctions the conformer can now reliably be predicted based on the sequence around the junction. The Holliday junction structure provides insights into how proteins can recognize these entities in a structure-specific manner.

References and and Footnotes
  1. Bernd N.M. van Buuren, Franc J.J. Overmars, Johannes H. Ippel, Cornelis Altona, and Sybren S. Wijmenga, "Solution structure of a DNA Three-Way junction containing two unpaired thymidines. Identification of sequence features that decide conformer selection.", J. Mol. Biol. 304(3), 371-83 (2000).
  2. Bernd N.M. van Buuren, Juergen Schleucher, and Sybren S. Wijmenga, "The solution structure of a model Holliday junction", to be submitted;
  3. Sybren S. Wijmenga, and Bernd N.M. van Buuren "The use of NMR methods for conformational studies of Nucleic Acids", Progress in NMR Spectroscopy, 32, 287-387 (1998)
  4. Bernd N.M. van Buuren, J?rgen Schleucher, and Sybren S. Wijmenga, "NMR structural studies on a DNA Four-Way Junction: Stacking preference and localization of the metal-ion binding site", J. Biomol. Struct. & Dyn. C 11, 237-243 (2000)
  5. Bernd N.M. van Buuren, Thomas Hermann, Sybren S. Wijmenga, and Eric Westhof, "Brownian dynamics simulations of metal-ion binding to four-way junctions", to be submitted.

Bernd van Buuren, Juergen Schleucher, and Sybren Wijmenga

Department of medical Biosciences, Medical Biophysics, Umea University, S 90 187 Umea, Sweden
phone:+46-90-7867403/7725; fax:+46-90-136310; Sybren.Wijmenga@chem.umu.se