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Published online 15 January 2004

Nucleic Acids Research, 2004, Vol. 32, No. 1 354-360
© 2004 Oxford University Press

Triplex-forming oligonucleotide target sequences in the human genome

J. Ramon Goñi1, Xavier de la Cruz1,2 and Modesto Orozco*,1,3

1 Molecular Modelling and Bioinformatics Unit, Institut de Recerca Biomédica, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, 2 Institució Catalana per la Recerca i Estudis Avançats (ICREA), Lluis Companys, 23, Barcelona 08028, Spain and 3 Departament de Bioquímica i Biologia Molecular, Facultat de Química, Martí i Franquès 1, Barcelona 08028, Spain

*To whom correspondence should be addressed. Tel: +34 93 403 71 55; Fax: +34 93 403 71 57; Email: modesto{at}mmb.pcb.ub.es
Correspondence may also be adddressed to Xavier de la Cruz. Tel: +34 93 403 71 55; Fax: +34 93 403 71 57; Email: xavier{at}mmb.pcb.ub.es

The existence of sequences in the human genome which can be a target for triplex formation, and accordingly are candidates for anti-gene therapies, has been studied by using bioinformatics tools. It was found that the population of triplex-forming oligonucleotide target sequences (TTS) is much more abundant than that expected from simple random models. The population of TTS is large in all the genome, without major differences between chromosomes. A wide analysis along annotated regions of the genome allows us to demonstrate that the largest relative concentration of TTS is found in regulatory regions, especially in promoter zones, which suggests a tremendous potentiality for triplex strategy in the control of gene expression. The dependence of the stability and selectivity of the triplexes on the length of the TTS is also analysed using knowledge-based rules.


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