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Journal of Nucleic Acids
Volume 2010, Article ID 431651, 8 pages
http://dx.doi.org/10.4061/2010/431651
Research Article

Effect of Base Sequence on G-Wire Formation in Solution

1Faculty of Mechanical Engineering, University of Maribor, Smetanova 17, 2000 Maribor, Slovenia
2J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
3Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
4Faculty of Life and Health Sciences, University of Ulster, Cromore Road, Northern Ireland, Coleraine BT52 1SA, UK

Received 1 February 2010; Accepted 22 March 2010

Academic Editor: R. Eritja

Copyright © 2010 Lea Spindler et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The formation and dimensions of G-wires by different short G-rich DNA sequences in solution were investigated by dynamic light scattering (DLS) and polyacrilamide gel electrophoresis (PAGE). To explore the basic principles of wire formation, we studied the effects of base sequence, method of preparation, temperature, and oligonucleotide concentration. Both DLS and PAGE show that thermal annealing induces much less macromolecular self-assembly than dialysis. The degree of assembly and consequently length of G-wires (5-6 nm) are well resolved by both methods for DNA sequences with intermediate length, while some discrepancies appear for the shortest and longest sequences. As expected, the longest DNA sequence gives the longest macromolecular aggregates with a length of about 11 nm as estimated by DLS. The quadruplex topologies show no concentration dependence in the investigated DNA concentration range (0.1 mM–0.4 mM) and no structural change upon heating.