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Journal of Nucleic Acids
Volume 2010, Article ID 763658, 11 pages
http://dx.doi.org/10.4061/2010/763658
Research Article

Structural Properties of G,T-Parallel Duplexes

1Institute for Research in Biomedicine, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Edifici Helix, Baldiri Reixac 15, 08028 Barcelona, Spain
2Joint IRB-BSC Program on Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
3Department of Analytical Chemistry, University of Barcelona, Diagonal 647, 08028 Barcelona, Spain
4Department of Spectroscopy and Molecular Structure, Instituto de Química Física Rocasolano, C.S.I.C. Serrano 119, 28006 Madrid, Spain

Received 19 August 2009; Accepted 15 November 2009

Academic Editor: Luis A. Marky

Copyright © 2010 Anna Aviñó 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 structure of G,T-parallel-stranded duplexes of DNA carrying similar amounts of adenine and guanine residues is studied by means of molecular dynamics (MD) simulations and UV- and CD spectroscopies. In addition the impact of the substitution of adenine by 8-aminoadenine and guanine by 8-aminoguanine is analyzed. The presence of 8-aminoadenine and 8-aminoguanine stabilizes the parallel duplex structure. Binding of these oligonucleotides to their target polypyrimidine sequences to form the corresponding G,T-parallel triplex was not observed. Instead, when unmodified parallel-stranded duplexes were mixed with their polypyrimidine target, an interstrand Watson-Crick duplex was formed. As predicted by theoretical calculations parallel-stranded duplexes carrying 8-aminopurines did not bind to their target. The preference for the parallel-duplex over the Watson-Crick antiparallel duplex is attributed to the strong stabilization of the parallel duplex produced by the 8-aminopurines. Theoretical studies show that the isomorphism of the triads is crucial for the stability of the parallel triplex.