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Open Access Research article

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions

Josep Ramon Goñi1, Juan Manuel Vaquerizas2, Joaquin Dopazo23 and Modesto Orozco145*

Author Affiliations

1 Molecular Modeling and Bioinformatics Unit. Institut de Recerca Biomèdica. Parc Científic de Barcelona. Josep Samitier 1-5. Barcelona 08028. Spain

2 Department of Bioinformatics, Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, Valencia, 46013, Spain

3 Functional Genomics Node, Instituto Nacional de Bioinfomatica, Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, Valencia 46013, Spain

4 Departament de Bioquímica i Biología Molecular. Facultat de Química. Universitat de Barcelona. Martí i Franquès 1. Barcelona 08028. Spain

5 Protein Structure and Modeling Node. Instituto Nacional de Bioinfomàtica. Genoma España. Parc Científic de Barcelona. Josep Samitier 1-5. Barcelona 08028. Spain

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BMC Genomics 2006, 7:63  doi:10.1186/1471-2164-7-63

Published: 27 March 2006

Abstract

Background

DNA duplex sequences that can be targets for triplex formation are highly over-represented in the human genome, especially in regulatory regions.

Results

Here we studied using bioinformatics tools several properties of triplex target sequences in an attempt to determine those that make these sequences so special in the genome.

Conclusion

Our results strongly suggest that the unique physical properties of these sequences make them particularly suitable as "separators" between protein-recognition sites in the promoter region.